MODULATION OF CELL FUNCTION FOR IMMUNOTHERAPY
Embodiments relate to a modified cell comprising an antigen binding molecule, and the expression and/or function of one or more genes in the modified cell has been enhanced or reduced or eliminated. The one or more genes include CXCR3, SLC1A3, YAP, TIGIT, S1P1, and IL-35. In embodiments, the cell is a T cell, a dendritic cell, a NK cell, or a macrophage cell. In embodiments, the antigen binding molecule comprises a chimeric antigen receptor (CAR) and/or the second antigen binding molecule is a T Cell Receptor (TCR).
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This application claims the benefit of U.S. Provisional Application 62/725,895, filed on Aug. 31, 2018, which is hereby incorporated by reference in its entirety.
SEQUENCE LISTING INFORMATIONA computer readable textfile, entitled “SDS1.0062US Sequence Listing_ST25.K” created on or about Aug. 14, 2019, with a file size of about 320 KB, contains the sequence listing for this application and is hereby incorporated by reference in its entirety.
TECHNICAL FIELDThe present disclosure relates to compositions and methods of using CAR T cell therapy to treat diseases including cancer.
BACKGROUNDT cells genetically targeted to certain malignancies have demonstrated tremendous clinical outcomes. During CAR-T cell therapy, physicians draw patients' blood and harvest her cytotoxic T cells. The cells are re-engineered in a lab to attack her particular cancer. Recent progress in genome editing technologies allow scientists to disrupt gene expression in T-cells in order to enhance effector functions or to bypass tumor immune suppression and metabolically hostile tumor microenvironment. Thus, there is a need to modulate T cell to overcome these problems.
SUMMARYEmbodiments relate to a modified cell comprising an antigen binding molecule, and expression and/or function of one or more genes in the modified cell has been enhanced or reduced or eliminated. The one or more genes include CXCR3, SLC1A3, YAP, TIGIT, S1P1, and IL-35. In embodiments, the cell is a T cell, a dendritic cell, a NK cell, or a macrophage cell. In embodiments, the antigen binding molecule comprises a chimeric antigen receptor (CAR) and/or the second antigen binding molecule is a T Cell Receptor (TCR).
This Summary is not intended to identify key features or essential features of the claimed subject matter, nor is it intended to be used to limit the scope of the claimed subject matter.
The Detailed Description is described with reference to the accompanying figures. The use of the same reference numbers in different figures indicates similar or identical items.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by those of ordinary skill in the art to which the disclosure belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, preferred methods and materials are described. For the purposes of the present disclosure, the following terms are defined below.
The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.
By “about” is meant a quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length that varies by as much as 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1% to a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length.
The term “activation,” as used herein, refers to the state of a cell that has been sufficiently stimulated to induce detectable cellular proliferation. Activation can also be associated with induced cytokine production and detectable effector functions. The term “activated T cells” refers to, among other things, T cells that are undergoing cell division.
The term “antibody” is used in the broadest sense and refers to monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multi-specific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired biological activity or function. The antibodies in the present disclosure may exist in a variety of forms including, for example, polyclonal antibodies, monoclonal antibodies, Fv, Fab and F(ab)2, as well as single chain antibodies and humanized antibodies (Harlow et al., 1999, In: Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, NY; Harlow et al., 1989, In: Antibodies: A Laboratory Manual, Cold Spring Harbor, New York; Houston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; Bird et al., 1988, Science 242:423-426).
The term “antibody fragments” refers to a portion of a full length antibody, for example, the antigen binding or variable region of the antibody. Other examples of antibody fragments include Fab, Fab′, F(ab′)2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multi-specific antibodies formed from antibody fragments.
The term “Fv” refers to the minimum antibody fragment which contains a complete antigen-recognition and -binding site. This fragment consists of a dimer of one heavy- and one light-chain variable region domain in tight, non-covalent association. From the folding of these two domains emanates six hypervariable loops (3 loops each from the H and L chain) that contribute the amino acid residues for antigen binding and confer antigen binding specificity to the antibody. However, even a single variable domain (or half of a Fv including only three complementarity determining regions (CDRs) specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site (the dimer).
An “antibody heavy chain,” as used herein, refers to the larger of the two types of polypeptide chains present in all antibody molecules in their naturally occurring conformations. An “antibody light chain,” as used herein, refers to the smaller of the two types of polypeptide chains present in all antibody molecules in their naturally occurring conformations. K and A light chains refer to the two major antibody light chain isotypes.
The term “synthetic antibody” refers to an antibody which is generated using recombinant DNA technology, such as, for example, an antibody expressed by a bacteriophage. The term also includes an antibody which has been generated by the synthesis of a DNA molecule encoding the antibody and the expression of the DNA molecule to obtain the antibody, or to obtain an amino acid encoding the antibody. The synthetic DNA is obtained using technology that is available and well known in the art.
The term “antigen” refers to a molecule that provokes an immune response, which may involve either antibody production, or the activation of specific immunologically-competent cells, or both. Antigens include any macromolecule, including all proteins or peptides, or molecules derived from recombinant or genomic DNA. For example, DNA including a nucleotide sequence or a partial nucleotide sequence encoding a protein or peptide that elicits an immune response, and therefore, encodes an “antigen” as the term is used herein. An antigen need not be encoded solely by a full-length nucleotide sequence of a gene. An antigen can be generated, synthesized or derived from a biological sample including a tissue sample, a tumor sample, a cell, or a biological fluid.
The term “anti-tumor effect” as used herein, refers to a biological effect associated with a decrease in tumor volume, a decrease in the number of tumor cells, a decrease in the number of metastases, decrease in tumor cell proliferation, decrease in tumor cell survival, an increase in life expectancy of a subject having tumor cells, or amelioration of various physiological symptoms associated with the cancerous condition. An “anti-tumor effect” can also be manifested by the ability of the peptides, polynucleotides, cells, and antibodies in the prevention of the occurrence of tumor in the first place.
The term “auto-antigen” refers to an antigen mistakenly recognized by the immune system as being foreign. Auto-antigens include cellular proteins, phosphoproteins, cellular surface proteins, cellular lipids, nucleic acids, glycoproteins, including cell surface receptors.
The term “autologous” is used to describe a material derived from a subject which is subsequently re-introduced into the same subject.
The term “allogeneic” is used to describe a graft derived from a different subject of the same species. As an example, a donor subject may be a related or unrelated or recipient subject, but the donor subject has immune system markers which are similar to the recipient subject.
The term “xenogeneic” is used to describe a graft derived from an subject of a different species. As an example, the donor subject is from a different species than a recipient subject and the donor subject and the recipient subject can be genetically and immunologically incompatible.
The term “cancer” as used to refer to a disease characterized by the rapid and uncontrolled growth of aberrant cells. Cancer cells can spread locally or through the bloodstream and lymphatic system to other parts of the body. Examples of various cancers include breast cancer, prostate cancer, ovarian cancer, cervical cancer, skin cancer, pancreatic cancer, colorectal cancer, renal cancer, liver cancer, brain cancer, lymphoma, leukemia, lung cancer, and the like.
Throughout this specification, unless the context requires otherwise, the words “comprise,” “includes” and “including” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements.
The phrase “consisting of” is meant to include, and is limited to, whatever follows the phrase “consisting of.” Thus, the phrase “consisting of” indicates that the listed elements are required or mandatory and that no other elements may be present.
The phrase “consisting essentially of” is meant to include any elements listed after the phrase and can include other elements that do not interfere with or contribute to the activity or action specified in the disclosure for the listed elements. Thus, the phrase “consisting essentially of” indicates that the listed elements are required or mandatory, but that other elements are optional and may or may not be present depending upon whether or not they affect the activity or action of the listed elements.
The terms “complementary” and “complementarity” refer to polynucleotides (i.e., a sequence of nucleotides) related by the base-pairing rules. For example, the sequence “A-G-T,” is complementary to the sequence “T-C-A.” Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.
The term “corresponds to” or “corresponding to” refers to (a) a polynucleotide having a nucleotide sequence that is substantially identical or complementary to all or a portion of a reference polynucleotide sequence or encoding an amino acid sequence identical to an amino acid sequence in a peptide or protein; or (b) a peptide or polypeptide having an amino acid sequence that is substantially identical to a sequence of amino acids in a reference peptide or protein.
The term “co-stimulatory ligand,” refers to a molecule on an antigen presenting cell (e.g., an APC, dendritic cell, B cell, and the like) that specifically binds a cognate co-stimulatory molecule on a T cell, thereby providing a signal which, in addition to the primary signal provided by, for instance, binding of a TCR/CD3 complex with an MHC molecule loaded with peptide, mediates a T cell response, including at least one of proliferation, activation, differentiation, and other cellular responses. A co-stimulatory ligand can include B7-1 (CD80), B7-2 (CD86), PD-L1, PD-L2, 4-1BBL, OX40L, inducible co-stimulatory ligand (ICOS-L), intercellular adhesion molecule (ICAM), CD30L, CD40, CD70, CD83, HLA-G, MICA, MICB, HVEM, lymphotoxin beta receptor, 3/TR6, ILT3, ILT4, HVEM, a ligand for CD7, an agonist or antibody that binds the Toll ligand receptor and a ligand that specifically binds with B7-H3. A co-stimulatory ligand also includes, inter alia, an agonist or an antibody that specifically binds with a co-stimulatory molecule present on a T cell, such as CD27, CD28, 4-1BB, OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and a ligand that specifically binds CD83.
The term “co-stimulatory molecule” refers to the cognate binding partner on a T cell that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the T cell, such as proliferation. Co-stimulatory molecules include an MHC class I molecule, BTLA, and a Toll-like receptor.
The term “co-stimulatory signal” refers to a signal, which in combination with a primary signal, such as TCR/CD3 ligation, leads to T cell proliferation and/or upregulation or downregulation of key molecules. The terms “disease” and “condition” may be used interchangeably or may be different in that the particular malady or condition may not have a known causative agent (so that etiology has not yet been worked out), and it is therefore not yet recognized as a disease but only as an undesirable condition or syndrome, wherein a more or less specific set of symptoms have been identified by clinicians. The term “disease” is a state of health of a subject wherein the subject cannot maintain homeostasis, and wherein if the disease is not ameliorated then the subject's health continues to deteriorate. In contrast, a “disorder” in a subject is a state of health in which the animal is able to maintain homeostasis, but in which the animal's state of health is less favorable than it would be in the absence of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal's state of health.
The term “effective” refers to adequate to accomplish a desired, expected, or intended result. For example, an “effective amount” in the context of treatment may be an amount of a compound sufficient to produce a therapeutic or prophylactic benefit.
The term “encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence (except that a “T” is replaced by a “U”) and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.
The term “exogenous” refers to a molecule that does not naturally occur in a wild-type cell or organism but is typically introduced into the cell by molecular biological techniques. Examples of exogenous polynucleotides include vectors, plasmids, and/or man-made nucleic acid constructs encoding the desired protein. Wth regard to polynucleotides and proteins, the term “endogenous” or “native” refers to naturally-occurring polynucleotide or amino acid sequences that may be found in a given wild-type cell or organism. Also, a particular polynucleotide sequence that is isolated from a first organism and transferred to a second organism by molecular biological techniques is typically considered an “exogenous” polynucleotide or amino acid sequence with respect to the second organism. In specific embodiments, polynucleotide sequences can be “introduced” by molecular biological techniques into a microorganism that already contains such a polynucleotide sequence, for instance, to create one or more additional copies of an otherwise naturally-occurring polynucleotide sequence, and thereby facilitate overexpression of the encoded polypeptide.
In embodiments, the polynucleotide may integrate into the genome of the modified cell and descendants of the modified cell will also express the polynucleotide, resulting in a stably transfected modified cell. In embodiments, the modified cell may express the polynucleotide encoding the CAR but the polynucleotide does not integrate into the genome of the modified cell such that the modified cell expresses the transiently transfected polynucleotide for a finite period of time (e.g., several days), after which the polynucleotide is lost through cell division or other factors. For example, the polynucleotide is present in the modified cell in a recombinant DNA construct, in an mRNA, or in a viral vector, and/or the polynucleotide is an mRNA, which is not integrated into the genome of the modified cell.
The term “expression” refers to the transcription and/or translation of a particular nucleotide sequence driven by its promoter.
The term “expression vector” refers to a vector including a recombinant polynucleotide including expression control sequences operably linked to a nucleotide sequence to be expressed. An expression vector includes sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.
The term “homologous” refers to sequence similarity or sequence identity between two polypeptides or between two polynucleotides when a position in both of the two compared sequences is occupied by the same base or amino acid monomer subunit, e.g., if a position in each of two DNA molecules is occupied by adenine, then the molecules are homologous at that position. The percent of homology between two sequences is a function of the number of matching or homologous positions shared by the two sequences divided by the number of positions compared ×100. For example, if 6 of 10 of the positions in two sequences are matched or homologous then the two sequences are 60% homologous. By way of example, the DNA sequences ATTGCC and TATGGC share 50% homology. A comparison is made when two sequences are aligned to give maximum homology.
The term “immunoglobulin” or “Ig,” refers to a class of proteins, which function as antibodies. The five members included in this class of proteins are IgA, IgG, IgM, IgD, and IgE. IgA is the primary antibody that is present in body secretions, such as saliva, tears, breast milk, gastrointestinal secretions and mucus secretions of the respiratory and genitourinary tracts. IgG is the most common circulating antibody. IgM is the main immunoglobulin produced in the primary immune response in most subjects. It is the most efficient immunoglobulin in agglutination, complement fixation, and other antibody responses, and is important in defense against bacteria and viruses. IgD is the immunoglobulin that has no known antibody function but may serve as an antigen receptor. IgE is the immunoglobulin that mediates immediate hypersensitivity by causing the release of mediators from mast cells and basophils upon exposure to the allergen.
The term “isolated” refers to a material that is substantially or essentially free from components that normally accompany it in its native state. The material can be a cell or a macromolecule such as a protein or nucleic acid. For example, an “isolated polynucleotide,” as used herein, refers to a polynucleotide, which has been purified from the sequences which flank it in a naturally-occurring state, e.g., a DNA fragment which has been removed from the sequences that are normally adjacent to the fragment. Alternatively, an “isolated peptide” or an “isolated polypeptide” and the like, as used herein, refer to in vitro isolation and/or purification of a peptide or polypeptide molecule from its natural cellular environment, and from association with other components of the cell.
The term “substantially purified” refers to a material that is substantially frr from components that normally associated with it in its native state. For example, a substantially purified cell refers to a cell that has been separated from other cell types with which it is normally associated in its naturally occurring or native state. In some instances, a population of substantially purified cells refers to a homogenous population of cells. In other instances, this term refers simply to a cell that has been separated from the cells with which they are naturally associated in their natural state. In some embodiments, the cells are cultured in vitro. In other embodiments, the cells are not cultured in vitro.
In the context of the present disclosure, the following abbreviations for the commonly occurring nucleic acid bases are used. “A” refers to adenosine, “C” refers to cytosine, “G” refers to guanosine, “T” refers to thymidine, and “U” refers to uridine.
Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some version contain an intron(s).
The term “lentivirus” refers to a genus of the Retroviridae family. Lentiviruses are unique among the retroviruses in being able to infect non-dividing cells; they can deliver a significant amount of genetic information into the DNA of the host cell, so they are one of the most efficient methods of a gene delivery vector. Moreover, the use of lentiviruses enables integration of the genetic information into the host chromosome resulting in stably transduced genetic information. HIV, SIV, and FIV are all examples of lentiviruses. Vectors derived from lentiviruses offer the means to achieve significant levels of gene transfer in vivo.
The term “modulating,” refers to mediating a detectable increase or decrease in the level of a response in a subject compared with the level of a response in the subject in the absence of a treatment or compound, and/or compared with the level of a response in an otherwise identical but untreated subject. The term encompasses perturbing and/or affecting a native signal or response thereby mediating a beneficial therapeutic response in a subject, preferably, a human.
Nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
The term “under transcriptional control” refers to a promoter being operably linked to and in the correct location and orientation in relation to a polynucleotide to control the initiation of transcription by RNA polymerase and expression of the polynucleotide.
The term “overexpressed” tumor antigen or “overexpression” of the tumor antigen is intended to indicate an abnormal level of expression of the tumor antigen in a cell from a disease area such as a solid tumor within a specific tissue or organ of the patient relative to the level of expression in a normal cell from that tissue or organ. Patients having solid tumors or a hematological malignancy characterized by overexpression of the tumor antigen can be determined by standard assays known in the art.
The term “parenteral administration” of a composition includes, e.g., subcutaneous (s.c.), intravenous (i.v.), intramuscular (i.m.), intrasternal injection, or infusion techniques.
The terms “patient,” “subject,” and “individual,” and the like are used interchangeably herein, and refer to any human, animal, or living organism, amenable to the methods described herein. In certain non-limiting embodiments, the patient, subject, or individual is a human or animal. In some embodiments, the term “subject” is intended to include living organisms in which an immune response can be elicited (e.g., mammals). Examples of subjects include humans, and animals such as dogs, cats, mice, rats, and transgenic species thereof.
A subject in need of a treatment or in need thereof includes a subject having a disease, condition, or disorder that needs to be treated. A subject in need thereof also includes a subject that needs treatment for prevention of a disease, condition, or disorder.
The term “polynucleotide” or “nucleic acid” refers to mRNA, RNA, cRNA, rRNA, cDNA or DNA. The term typically refers to a polymeric form of nucleotides of at least 10 bases in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide. The term includes all forms of nucleic acids including single and double stranded forms of nucleic acids.
The terms “polynucleotide variant” and “variant” and the like refer to polynucleotides displaying substantial sequence identity with a reference polynucleotide sequence or polynucleotides that hybridize with a reference sequence under stringent conditions that are defined hereinafter. These terms also encompass polynucleotides that are distinguished from a reference polynucleotide by the addition, deletion or substitution of at least one nucleotide. Accordingly, the terms “polynucleotide variant” and “variant” include polynucleotides in which one or more nucleotides have been added or deleted or replaced with different nucleotides. In this regard, it is well understood in the art that certain alterations inclusive of mutations, additions, deletions, and substitutions can be made to a reference polynucleotide whereby the altered polynucleotide retains the biological function or activity of the reference polynucleotide or has increased activity in relation to the reference polynucleotide (i.e., optimized). Polynucleotide variants include, for example, polynucleotides having at least 50% (and at least 51% to at least 99% and all integer percentages in between, e.g., 90%, 95%, or 98%) sequence identity with a reference polynucleotide sequence described herein. The terms “polynucleotide variant” and “variant” also include naturally-occurring allelic variants and orthologs.
The terms “polypeptide,” “polypeptide fragment,” “peptide,” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues and to variants and synthetic analogues of the same. Thus, these terms apply to amino acid polymers in which one or more amino acid residues are synthetic non-naturally occurring amino acids, such as a chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally-occurring amino acid polymers. In certain aspects, polypeptides may include enzymatic polypeptides, or “enzymes,” which typically catalyze (i.e., increase the rate of) various chemical reactions.
The term “polypeptide variant” refers to polypeptides that are distinguished from a reference polypeptide sequence by the addition, deletion, or substitution of at least one amino acid residue. In certain embodiments, a polypeptide variant is distinguished from a reference polypeptide by one or more substitutions, which may be conservative or non-conservative. In certain embodiments, the polypeptide variant comprises conservative substitutions and, in this regard, it is well understood in the art that some amino acids may be changed to others with broadly similar properties without changing the nature of the activity of the polypeptide. Polypeptide variants also encompass polypeptides in which one or more amino acids have been added or deleted or replaced with different amino acid residues.
The term “promoter” refers to a DNA sequence recognized by the synthetic machinery of the cell or introduced synthetic machinery, required to initiate the specific transcription of a polynucleotide sequence. The term “expression control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
The term “bind,” “binds,” or “interacts with” refers to a molecule recognizing and adhering to a particular second molecule in a sample or organism but does not substantially recognize or adhere to other structurally unrelated molecules in the sample. The term “specifically binds,” as used herein with respect to an antibody, refers to an antibody which recognizes a specific antigen, but does not substantially recognize or bind other molecules in a sample. For example, an antibody that specifically binds an antigen from one species may also bind that antigen from one or more species. But, such cross-species reactivity does not itself alter the classification of an antibody as specific. In another example, an antibody that specifically binds an antigen may also bind different allelic forms of the antigen. However, such cross reactivity does not itself alter the classification of an antibody as specific. In some instances, the terms “specific binding” or “specifically binding,” can be used in reference to the interaction of an antibody, a protein, or a peptide with a second chemical species, to mean that the interaction is dependent upon the presence of a particular structure (e.g., an antigenic determinant or epitope) on the chemical species; for example, an antibody recognizes and binds a specific protein structure rather than to any protein. If an antibody is specific for epitope “A,” the presence of a molecule containing epitope A (or free, unlabeled A), in a reaction containing labeled “A” and the antibody, will reduce the amount of labeled A bound to the antibody.
A “binding protein” is a protein that is able to bind non-covalently to another molecule. A binding protein can bind to, for example, a DNA molecule (a DNA-binding protein), an RNA molecule (an RNA-binding protein) and/or a protein molecule (a protein-binding protein). In the case of a protein-binding protein, it can bind to itself (to form homodimers, homotrimers, etc.) and/or it can bind to one or more molecules of a different protein or proteins. A binding protein can have more than one type of binding activity. For example, zinc finger proteins have DNA-binding, RNA-binding, and protein-binding activity.
A “zinc finger DNA binding protein” (or binding domain) is a protein, or a domain within a larger protein, that binds DNA in a sequence-specific manner through one or more zinc fingers, which are regions of amino acid sequence within the binding domain whose structure is stabilized through coordination of a zinc ion. The term zinc finger DNA binding protein is often abbreviated as zinc finger protein or ZFP.
Zinc finger binding domains can be “engineered” to bind to a predetermined nucleotide sequence, for example via engineering (altering one or more amino acids) of the recognition helix region of a naturally occurring zinc finger protein. Further, a Zinc finger binding domain may be fused a DNA-cleavage domain to form a Zinc finger nuclease (ZFN) targeting a specific desired DNA sequence. For example, a pair of ZFNs (e.g., a ZFN-left arm and a ZFN-right arm) may be engineered to target and cause modifications of specific desired DNA sequences (e.g., TRAC genes), as illustrated in
“Cleavage” refers to the breakage of the covalent backbone of a DNA molecule. Cleavage can be initiated by a variety of methods including, but not limited to, enzymatic or chemical hydrolysis of a phosphodiester bond. Both single-stranded cleavage and double-stranded cleavage are possible, and double-stranded cleavage can occur as a result of two distinct single-stranded cleavage events. DNA cleavage can result in the production of either blunt ends or staggered ends. In certain embodiments, fusion polypeptides are used for targeted double-stranded DNA cleavage.
A “target site” or “target sequence” is a nucleic acid sequence that defines a portion of a nucleic acid to which a binding molecule will bind, provided sufficient conditions for binding exist. For example, the sequence 5′ GAATTC 3′ is a target site for the Eco RI restriction endonuclease. Exemplary target sites for various targeted ZFPs are shown in Table 1.
A “fusion” molecule is a molecule in which two or more subunit molecules are linked, preferably covalently. The subunit molecules can be the same chemical type of molecule or can be different chemical types of molecules. Examples of the first type of fusion molecule include, but are not limited to, fusion proteins (for example, a fusion between a ZFP DNA-binding domain and one or more activation domains) and fusion nucleic acids (for example, a nucleic acid encoding the fusion protein described supra). Examples of the second type of fusion molecule include, but are not limited to, a fusion between a triplex-forming nucleic acid and a polypeptide, and a fusion between a minor groove binder and a nucleic acid.
Expression of a fusion protein in a cell can result from delivery of the fusion protein to the cell or by delivery of a polynucleotide encoding the fusion protein to a cell, wherein the polynucleotide is transcribed, and the transcript is translated, to generate the fusion protein. Trans-splicing, polypeptide cleavage, and polypeptide ligation can also be involved in the expression of the protein in a cell. Methods for polynucleotide and polypeptide delivery to cells are presented elsewhere in this disclosure.
“Modulation” of gene expression refers to a change in the activity of a gene. Modulation of expression can include but is not limited to, gene activation and gene repression. Genome editing (e.g., cleavage, alteration, inactivation, random mutation) can be used to modulate expression. Gene inactivation refers to any reduction in gene expression as compared to a cell that does not include a ZFP as described herein. Thus, gene inactivation may be partial or complete.
A “region of interest” is any region of cellular chromatin, such as, for example, a gene or a non-coding sequence within or adjacent to a gene, in which it is desirable to bind an exogenous molecule. Binding can be for the purposes of targeted DNA cleavage and/or targeted recombination. A region of interest can be present in a chromosome, an episome, an organellar genome (e.g., mitochondrial, chloroplast), or an infecting viral genome, for example. A region of interest can be within the coding region of a gene, within transcribed non-coding regions such as, for example, leader sequences, trailer sequences or introns, or within non-transcribed regions, either upstream or downstream of the coding region. A region of interest can be as small as a single nucleotide pair or up to 2,000 nucleotide pairs in length, or any integral value of nucleotide pairs.
By “statistically significant,” it is meant that the result was unlikely to have occurred by chance. Statistical significance can be determined by any method known in the art. Commonly used measures of significance include the p-value, which is the frequency or probability with which the observed event would occur if the null hypothesis were true. If the obtained p-value is smaller than the significance level, then the null hypothesis is rejected. In simple cases, the significance level is defined at a p-value of 0.05 or less. A “decreased” or “reduced” or “lesser” amount is typically a “statistically significant” or a physiologically significant amount, and may include a decrease that is about 1.1, 1.2, 1.3, 1.4, 1.5, 1.6 1.7, 1.8, 1.9, 2, 2.5, 3, 3.5, 4, 4.5, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 or more times (e.g., 100, 500, 1000 times) (including all integers and decimal points in between and above 1, e.g., 1.5, 1.6, 1.7. 1.8, etc.) an amount or level described herein.
The term “stimulation,” refers to a primary response induced by binding of a stimulatory molecule (e.g., a TCR/CD3 complex) with its cognate ligand thereby mediating a signal transduction event, such as signal transduction via the TCR/CD3 complex. Stimulation can mediate altered expression of certain molecules, such as downregulation of TGF-β, and/or reorganization of cytoskeletal structures. CD3 zeta is not the only suitable primary signaling domain for a CAR construct with respect to the primary response. For example, back in 1993, both CD3 zeta and FcR gamma were shown as functional primary signaling domains of CAR molecules. Eshhar et al., “Specific activation and targeting of cytotoxic lymphocytes through chimeric single chains consisting of antibody-binding domains and the gamma or zeta subunits of the immunoglobulin and T-cell receptors” PNAS, 1993 Jan. 15; 90(2):720-4, showed that two CAR constructs in which an scFv was fused to “either the FcR y chain or the CD3 complex s chain” triggered T cell activation and target cell. Notably, as demonstrated in Eshhar et al., CAR constructs containing only the primary signaling domain CD3 zeta or FcR gamma are functional without the co-presence of co-stimulatory domains. Additional non-CD3 zeta based CAR constructs have been developed over the years. For example, Wang et al., “A Chimeric Antigen Receptor (CARs) Based Upon a Killer Immunoglobulin-Like Receptor (KIR) Triggers Robust Cytotoxic Activity in Solid Tumors” Molecular Therapy, vol. 22, no. Suppl.1, May 2014, page S57, tested a CAR molecule in which an scFv was fused to “the transmembrane and cytoplasmic domain of a killer immunoglobulin-like receptor (KIR). Wang et al. states that, “a KIR-based CAR targeting mesothelin (SS 1-KIR) triggers antigen-specific cytotoxic activity and cytokine production that is comparable to CD3˜-based CARs.” A second publication from the same group, Wang et al., “Generation of Potent T-cell Immunotherapy for Cancer Using DAP12-Based, Multichain, Chimeric Immunoreceptors” Cancer Immunol Res. 2015 Jul;3(7):815-26, showed that a CAR molecule in which “a single-chain variable fragment for antigen recognition [was fused] to the transmembrane and cytoplasmic domains of KIR2DS2, a stimulatory killer immunoglobulin-like receptor (KIR)” functioned both in vitro and in vivo “when introduced into human T cells with DAP12, an immunotyrosine-based activation motifs-containing adaptor.”
The term “stimulatory molecule” refers to a molecule on a T cell that specifically binds a cognate stimulatory ligand present on an antigen presenting cell. For example, a functional signaling domain derived from a stimulatory molecule is the zeta chain associated with the T cell receptor complex.
The term “stimulatory ligand” refers to a ligand that when present on an antigen presenting cell (e.g., an APC, a dendritic cell, a B-cell, and the like.) can specifically bind with a cognate binding partner (referred to herein as a “stimulatory molecule”) on a cell, for example a T cell, thereby mediating a primary response by the T cell, including activation, initiation of an immune response, proliferation, and similar processes. Stimulatory ligands are well-known in the art and encompass, inter alia, an MHC Class I molecule loaded with a peptide, an anti-CD3 antibody, a superagonist anti-CD28 antibody, and a superagonist anti-CD2 antibody.
The term “therapeutic” refers to a treatment and/or prophylaxis. A therapeutic effect is obtained by suppression, remission, or eradication of a disease state or alleviating the symptoms of a disease state.
The term “therapeutically effective amount” refers to the amount of the subject compound that will elicit the biological or medical response of a tissue, system, or subject that is being sought by the researcher, veterinarian, medical doctor or another clinician. The term “therapeutically effective amount” includes that amount of a compound that, when administered, is sufficient to prevent the development of, or alleviate to some extent, one or more of the signs or symptoms of the disorder or disease being treated. The therapeutically effective amount will vary depending on the compound, the disease and its severity and the age, weight, etc., of the subject to be treated.
The term “treat a disease” refers to the reduction of the frequency or severity of at least one sign or symptom of a disease or disorder experienced by a subject.
The term “transfected” or “transformed” or “transduced” refers to a process by which an exogenous nucleic acid is transferred or introduced into the host cell. A “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed, or transduced with exogenous nucleic acid. The cell includes the primary subject cell and its progeny.
The term “vector” refers to a polynucleotide that comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Numerous vectors are known in the art including linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “vector” includes an autonomously replicating plasmid or a virus. The term also includes non-plasmid and non-viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, polylysine compounds, liposomes, and the like. Examples of viral vectors include, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, and others. For example, lentiviruses are complex retroviruses, which, in addition to the common retroviral genes gag, pol, and env, contain other genes with regulatory or structural function. Lentiviral vectors are well known in the art. Some examples of lentivirus include the Human Immunodeficiency Viruses: HIV-1, HIV-2, and the Simian Immunodeficiency Virus: SIV. Lentiviral vectors have been generated by multiply attenuating the HIV virulence genes, for example, the genes env, vif, vpr, vpu, and nef are deleted making the vector biologically safe.
Ranges: throughout this disclosure, various aspects of the disclosure can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the disclosure. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range.
Embodiments relate to a modified cell comprising: an antigen binding molecule; and a disruption in an endogenous gene or an addition of an exogenous gene that are associated with a biosynthesis or transportation pathway of at least one of CXCR3, SLC1A3, YAP, TIGIT, S1P1, and IL-35. In some embodiments, the cell is a T cell, a dendritic cell, a NK cell, or a macrophage cell. In some embodiments, the antigen binding molecule comprises a chimeric antigen receptor (CAR) and/or the second antigen binding molecule is a T Cell Receptor (TCR).
Modified T-cells may be derived from a stem cell. The stem cells may be adult stem cells, embryonic stem cells, more particularly non-human stem cells, cord blood stem cells, progenitor cells, bone marrow stem cells, induced pluripotent stem cells, totipotent stem cells or hematopoietic stem cells. A modified cell may also be a dendritic cell, a NK-cell, a B-cell or a T-cell selected from the group consisting of inflammatory T-lymphocytes, cytotoxic T-lymphocytes, regulatory T-lymphocytes or helper T-lymphocytes. In another embodiment, Modified cells may be derived from the group consisting of CD4+T-lymphocytes and CD8+T-lymphocytes. Prior to expansion and genetic modification of the cells of the invention, a source of cells may be obtained from a subject through a variety of non-limiting methods. T cells may be obtained from a number of non-limiting sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors. In certain embodiments of the present invention, any number of T cell lines available and known to those skilled in the art, may be used. In embodiments, modified cells may be derived from a healthy donor, from a patient diagnosed with cancer or from a patient diagnosed with an infection. In embodiments, modified cell is part of a mixed population of cells which present different phenotypic characteristics.
The term “stem cell” refers to any of certain types of cell which have the capacity for self-renewal and the ability to differentiate into other kind(s) of cell. For example, a stem cell gives rise either to two daughter stem cells (as occurs in vitro with embryonic stem cells in culture) or to one stem cell and a cell that undergoes differentiation (as occurs e.g. in hematopoietic stem cells, which give rise to blood cells). Different categories of stem cell may be distinguished on the basis of their origin and/or on the extent of their capacity for differentiation into other types of cell. For example, stem cell may include embryonic stem (ES) cells (i.e., pluripotent stem cells), somatic stem cells, Induced pluripotent stem cells, and any other types stem cells.
The pluripotent embryonic stem cells may be found in the inner cell mass of a blastocyst and have high innate capacity for differentiation. For example, pluripotent embryonic stem cells may have the potential to form any type of cell in the body. When grown in vitro for long periods of time, ES cells maintain pluripotency: progeny cells retain the potential for multilineage differentiation.
Somatic stem cells may include the fetal stem cells (from the fetus) and adult stem cells (found in various tissues, such as bone marrow). These cells have been regarded as having a capacity for differentiation lower than that of the pluripotent ES cells—with the capacity of fetal stem cells being greater than that of adult stem cells; they apparently differentiate into only a limited range of types of cell and have been described as multipotent. The ‘tissue-specific’ stem cells normally give rise to only one type of cell. For example, embryonic stem cells may be differentiated into blood stem cells (e.g., Hematopoietic stem cells (HSCs)), which may be further differentiated into various blood cells (e.g., red blood cells, platelets, white blood cells, etc.).
Induced pluripotent stem cells (i.e., iPS cells or iPSCs) may include a type of pluripotent stem cell artificially derived from a non-pluripotent cell (e.g., an adult somatic cell) by inducing a expression of specific genes. Induced pluripotent stem cells are similar to natural pluripotent stem cells, such as embryonic stem (ES) cells, in many aspects, such as the expression of certain stem cell genes and proteins, chromatin methylation patterns, doubling time, embryoid body formation, teratoma formation, viable chimera formation, and potency and differentiability. Induced pluripotent cells may be made from adult stomach, liver, skin cells and blood cells.
In embodiments, the modified cell is a T cell, NK cell, dendritic cell, or a macrophage.
In some embodiments, the antigen binding molecule is the CAR comprising an extracellular domain, a transmembrane domain, and an intracellular domain, the extracellular domain binds an antigen.
In some embodiments, the intracellular domain comprises a co-stimulatory signaling region that comprises an intracellular domain of a co-stimulatory molecule selected from the group consisting of CD27, CD28, 4-1BB, OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and any combination thereof. In some embodiments, the antigen is Epidermal growth factor receptor (EGFR), Variant III of the epidermal growth factor receptor (EGFRvIII), Human epidermal growth factor receptor 2 (HER2), Mesothelin (MSLN), Prostate-specific membrane antigen (PSMA), Carcinoembryonic antigen (CEA), Disialoganglioside 2 (GD2), Interleukin-13Ra2 (IL13Rα2), Glypican-3 (GPC3), Carbonic anhydrase IX (CAIX), L1 cell adhesion molecule (L1-CAM), Cancer antigen 125 (CA125), Cluster of differentiation 133 (CD133), Fibroblast activation protein (FAP), Cancer/testis antigen 1B (CTAG1B), Mucin 1 (MUC1), Folate receptor-α (FR-α) CD19, FZD10, TSHR, PRLR, Muc 17, GUCY2C, CD207, CD3, CD5, B-Cell Maturation Antigen (BCMA), or CD4.
In some embodiments, the antigen binding molecule is a modified TCR. In some embodiments, the TCR is derived from spontaneously occurring tumor-specific T cells in patients. In some embodiments, the TCR binds to a tumor antigen. In some embodiments, the tumor antigen comprises CEA, gp100, MART-1, p53, MAGE-A3, or NY-ESO-1. In some embodiments, the TCR comprises TCRγ and TCRδ Chains or TCRα and TCRβ chains, or a combination thereof. In some embodiments, the TCR comprises TCRγ and TCRδ Chains or TCRα and TCRβ chains. In some embodiments, a T cell clone that expresses a TCR with high affinity for the target antigen may be isolated. In certain embodiments, tumor-infiltrating lymphocytes (TILs) or peripheral blood mononuclear cells (PBMCs) may be cultured in the presence of antigen-presenting cells (APCs) pulsed with a peptide representing an epitope known to elicit a dominant T cell response when presented in the context of a defined HLA allele. High-affinity clones may be then selected on the basis of MHC-peptide tetramer staining and/or the ability to recognize and lyse target cells pulsed with low titrated concentrations of cognate peptide antigen. After the clone has been selected, the TCRα and TCRβ chains or TCRγ and TCRδ Chains are identified and isolated by molecular cloning. For example, for TCRα and TCRβ chains, the TCRα and TCRβ gene sequences are then used to generate an expression construct that ideally promotes stable, high-level expression of both TCR chains in human T cells. The transduction vehicle (e.g., a gammaretrovirus or lentivirus) may be then generated and tested for functionality (antigen specificity and functional avidity) and used to produce a clinical lot of the vector. An aliquot of the final product is then used to transduce the target T cell population (generally purified from patient PBMCs), which is expanded before infusion into the patient. Various methods may be implemented to obtain genes encoding tumor-reactive TCR. More information is provided in Kershaw et al., Clin Transl Immunology. 2014 May; 3(5): e16.
In some embodiments, specific TCR can be derived from spontaneously occurring tumor-specific T cells in patients. Antigens included in this category include the melanocyte differentiation antigens MART-1 and gp100, as well as the MAGE antigens and NY-ESO-1, with expression in a broader range of cancers. TCRs specific for viral-associated malignancies can also be isolated, as long as viral proteins are expressed by transformed cells. Malignancies in this category include liver and cervical cancer, associated with hepatitis and papilloma viruses, and Epstein-Barr virus-associated malignancies. In some embodiments, target antigens of the TCR may include CEA (e.g., for colorectal cancer), gp100, MART-1, p53 (e.g., for Melanoma), MAGE-A3 (e.g., Melanoma, esophageal and synovial sarcoma), NY-ESO-1 (e.g., for Melanoma and sarcoma as well as Multiple myelomas).
Some embodiments relate to the cell that has the disruption in an endogenous gene associated with a biosynthesis or transportation pathway of CXCR2 and a reduced amount of CXCR2 as compared to the corresponding wild-type of the cell. In some embodiments, the disruption is made by a nuclease.
In some embodiments, the disruption is made by a zinc finger nuclease (ZFN). In some embodiments, the disruption is made by a CRISPR associated protein 9 (Cas9). In some embodiments, the disruption is made by a Transcription activator-like effector nuclease (TALEN). In some embodiments, a target sequence of the TALEN is the amino acid sequence SEQ ID No: 29, or a left arm of the TALEN is the amino acid sequence SEQ ID No: 30, and a right arm of the TALEN is the amino acid sequence SEQ ID No: 31. In some embodiments, a target sequence of the TALEN is the amino acid sequence SEQ ID No: 32, or a left arm of the TALEN is the amino acid sequence SEQ ID No: 33, and a right arm of the TALEN is the amino acid sequence SEQ ID No: 34. In some embodiments, a target sequence of the TALEN is the amino acid sequence SEQ ID No: 35, or a left arm of the TALEN is the amino acid sequence SEQ ID No: 36, and a right arm of the TALEN is the amino acid sequence SEQ ID No: 37.
Some embodiments relate to the cell that has a nucleic acid sequence encoding modified CXCR2 that lacks a functional intracellular domain as compared to the corresponding wild-type receptor. In some embodiments, the modified CXCR2 is a dominant negative variant of CXCR2 such that the cell has an altered molecular function of CXCR2. In some embodiments, an intracellular domain of the modified CXCR2 consisting essentially of the amino acid sequence SEQ ID NO: 5 or comprising the amino acid sequence SEQ ID NO: 6.
Some embodiments relate to the cell that has the enhancement in an endogenous gene associated with a biosynthesis or transportation pathway of CXCR3 and an increased amount of CXCR2 as compared to the corresponding wild-type of the cell. In some embodiments, the CXCR3 is overexpressed as compared to the corresponding wild-type of the cell. In some embodiments, a level of expression of the CXCR3 is greater than the average level of expression of CXCR3 on the cell at least about 10%, 20%, 30%, 40%, or 50%. In some embodiments, the genome of the cell comprises a polynucleotide sequence encoding the CXCR3, the polynucleotide sequence operably linked to a promoter polynucleotide sequence. In some embodiments, the CAR an extracellular, a transmembrane domain; and an intracellular segment comprising a co-stimulatory domain and a CD3ζ intracellular signaling domain comprising a CXCL9/CXCL10-CXCR3 signaling motif such that CXCR3 overexpression is in an antigen-dependent manner.
CXCR2 is mainly expressed on the surface of cells such as neutrophils, monocytes, and T cells. It is a member of the G protein-coupled receptor superfamily and binds to CXCL1. CXCL1 can inhibit T cell infiltration of tumor microenvironment by binding to CXCR2 receptor. In some embodiments, CXCR2 can be expressed on the surface of T cells and bind to ligand CXCL1 to inhibit T cell infiltration in tumor microenvironment. By down-regulating the expression of CXCR2 in T cells, The CXCL1-CXCR2 signaling pathway inhibits the infiltration of T cells into the tumor microenvironment, thereby enhancing the effect of T cells, especially CAR-T cells, in immunotherapy. In some embodiments, the down-regulation of CXCR2 expression in T cells promotes the infiltration of T cells into the tumor microenvironment, and the modified CAR-T cells contribute to the improvement of immunotherapy. In some embodiments, the CXCR2 gene in T cells may be knocked out using a technique edited by Crisper et al., and T cells may be engineered into CXCR2-deficient CAR-T cells. In the mouse model, the efficacy of the modified CAR-T cells and common CAR-T cells may be compared, and the CXCR2-deficient CAR-T cells may be predicted to have a better tumor suppressing effect.
CXCR3 is mainly expressed on the surface of T cells, but not on related cells such as B cells, monocytes and granulocytes. CXCR3 and its ligand CXCL9/CXCL10 can help effect T cells to metastasize to tumor tissues, thereby achieving killing and control of tumor cells. CXCR3 can be expressed on the surface of T cells and binds to the ligand CXCL9/CXCL10 to promote T cell infiltration in the tumor microenvironment. The present invention enhances the promotion of T cell infiltration of the tumor microenvironment by overexpressing CXCR3 in T cells to enhance the CXCL9/CXCL10-CXCR3 signaling pathway. Role, thereby enhancing the effect of T cells, especially CAR-T cells, in immunotherapy.
Some embodiments relate to the cell that comprises a nucleic acid sequence encoding SLC1A3. In some embodiments, the cell comprises a nucleic acid sequence SEQ ID NO: Construct of SLC1A3-CART. In some embodiments, the cell has enhanced capability of uptake of glutamate.
Aspartic acid is one of the basic amino acids that make up proteins. It is ubiquitous in biosynthesis and is essential for cell life activities. Recent studies have shown that in the hypoxic tumor microenvironment, the level of aspartic acid in tumor cells is reduced, which is the main limiting factor for tumor proliferation. Therefore, limiting the level of aspartic acid in tumor cells can be used as a tumor treatment. The new direction. Studies have shown that in some tumor cells, aspartate to intracellular transport requires a special transporter SLC1A3. The present invention competes for aspartic acid in tumor cells by expressing the SLC1A3 gene in T cells to inhibit aspartate levels in tumor cells. This invention can inhibit tumor growth by limiting aspartic acid, thereby enhancing the effect of T cells, particularly CAR-T cells, in immunotherapy.
The level of aspartic acid in tumor cells is the main limiting factor for tumor proliferation, so limiting the level of aspartate in tumor cells can serve as a new direction for tumor therapy. In some tumor cells, aspartate to intracellular transport requires a special transporter SLC1A3. The present invention inhibits aspartate levels in tumor cells by expressing TLC1A3 gene in T cells such that T cells compete for aspartic acid in tumor cells. This invention can inhibit tumor growth by limiting the level of aspartic acid in the tumor, thereby enhancing the effect of T cells, particularly CAR-T cells, in immunotherapy. The present invention inhibits aspartate levels in tumor cells by expressing TLC1A3 gene in T cells such that T cells compete for aspartic acid in tumor cells. This invention can inhibit tumor growth by limiting aspartic acid in the tumor, thereby enhancing the effect of T cells, particularly CAR-T cells, in immunotherapy. First, a CAR-T cell capable of expressing the SLC1A3 gene may be constructed. The lentiviral vector and the lentiviral packaging plasmid (Gag-pol and VSV-G) expressing the cDNA of SLC1A3 may be transfected into HEK293T cells, and 48 hours after transfection, virus particles may be obtained, and the virus particles may be used to transfect CAR-T cells to obtain energy. CAR-T cells expressing the SLC1A3 gene. In the mouse model, the efficacy of the modified CAR-T cells and common CAR-T cells may be compared, and the CAR-T cells expressing SLC1A3 may be predicted to have a better tumor suppressing effect. Aspartic acid is a negatively charged amino acid in a physiological pH environment, and its intracellular transport requires a special transporter. In the human body, there are now 7 aspartate transporters from SLC1A1 to SLC1A7, most of which are expressed on the cell membrane of nerve cells. One of the aspartate transporters SLC1A3 can also be abundant in tumor epithelial cells. expression. SLC1A3 has a high aspartic acid affinity and can help tumor cells absorb aspartic acid to maintain nucleic acid synthesis and tumor growth.
Some embodiments relate to the cell that has a reduced amount of Yes-associated protein (YAP) as compared to a corresponding wild-type cell, wherein the modified cell has decreased Treg-mediated suppression of antitumor immunity as compared to the corresponding wild-type cell. In some embodiments, the modified T cell has a disruption in an endogenous gene associated with a biosynthesis or transportation pathway of YAP. In some embodiments, the disruption comprises a disruption of one or more exons of YAP gene. In some embodiments, the disruption of the one or more exons of YAP gene comprises a disruption of an exon of YAP gene having the nucleic acid sequence ID: 7. In some embodiments, the cell further comprises a TALEN targeting the nucleic acid sequence ID: 38. In some embodiments, the TALEN comprise a left arm comprising the nucleic acid sequence ID: 39 and a right arm comprising the nucleic acid SEQ ID NO: 40.
Some embodiments relate to the cell that has a nucleic acid sequence that encodes a modified receptor that directly or indirectly activate YAP activity, the modified receptor lacking a functional intracellular domain, and the modified receptor and the antigen binding molecule are expressed as gene products that are separate polypeptides. In some embodiments, the modified receptor is ERBB4, CD44, or a G12/13-coupled receptor that lacks a functional intracellular domain as compared to the corresponding wild-type receptor.
In some embodiments, the G12/13-coupled receptor comprises one of adrenergic receptor a1B, LPA receptors, purinergic receptors, 5-hydroxytryptamine receptor 4, muscarinic acetylcholine receptor M1, adenosine receptor A1A, angiontensin II receptor, free fatty acid receptor 1, platelet-activating factor receptor, thromboxane A2, frizzled homolog D4, complement component 3a receptor 1, estrogen receptor 1, glutamate receptor metabotropic 2, opioid receptor D1, secretin receptor, thyroid-stimulating hormone receptor, gastrin-releasing peptide receptor, melanocortin receptor 1, somatostatin receptor 1, prostaglandin E receptor 2, and bombesin-like receptor 3. In some embodiments, the modified receptor is a modified ERBB4. In some embodiments, the modified ERBB4 consist essentially of the nucleic acid sequence ID: 11. In some embodiments, the modified receptor is a modified LPAR1. In some embodiments, the modified LPAR1 consist essentially the nucleic acid sequence ID: 14. In some embodiments, the modified receptor is a modified CD44. In some embodiments, the modified CD44 consist essentially the nucleic acid sequence ID: 17. In some embodiments, the modified ERBB4 has a mutant site of tyrosine phosphorylation as compared to the corresponding wild-type receptor. In some embodiments, the modified receptor is a dominant negative of ERBB4 receptor. Dominant negative mutations have an altered gene product that acts antagonistically to the wild-type allele. These mutations usually result in an altered molecular function (often inactive) and are characterized by a dominant or semi-dominant phenotype. In some embodiments, the modified receptor is a dominant negative variant of a receptor of the ERBB4, CD44, or G12/13-coupled receptor.
Some embodiments relate to the cell that has a nucleic acid sequence encoding modified TIGIT that lacks a functional intracellular domain as compared to the corresponding wild-type receptor. In some embodiments, the modified TIGIT is a dominant negative variant of TIGIT such that the cell has an altered molecular function of TIGIT. In some embodiments, an intracellular domain of the modified TIGIT consisting essentially of the amino acid sequence SEQ ID NO: 19 or comprising the amino acid sequence SEQ ID: 20.
Some embodiments relate to the cell that comprises a nucleic acid sequence encoding S1P1. In some embodiments, the cell comprises a nucleic acid sequence SEQ ID NO: Construct of S1P1-CART.
Some embodiments relate to the cell that has a nucleic acid sequence encoding a modified IL-35 receptor that lacks a functional intracellular domain as compared to the corresponding wild-type receptor. In some embodiments, the modified IL-35 receptor is a dominant negative variant of IL-35 receptor such that the cell has an altered molecular function of IL-35 receptor. In some embodiments, the modified receptor is gp130 or IL-12Rβ2 receptor that lacks a functional intracellular domain as compared to the corresponding wild-type receptor. In some embodiments, an intracellular domain of the modified IL-35 receptor consisting essentially of the amino acid sequence SEQ ID NO: 24 or 27 or comprising the amino acid sequence SEQ ID NO: 25 or 28.
In some embodiments, the cell has the disruption in an endogenous gene associated with a biosynthesis or transportation pathway of spry1 and/or spry2 and a reduced amount of spry1 and/or spry2as compared to the corresponding wild-type of the cell. In some embodiments, the disruption is made by a nuclease. In some embodiments, the disruption is made by a CRISPR associated protein 9 (Cas9). In some embodiments, the disruption is made by a Transcription activator-like effector nuclease (TALEN). In some embodiments, the disruption is made by a zinc finger nuclease (ZFN). In some embodiments, a first target sequence of the ZFN is the amino acid sequence SEQ ID No: 74, and a second target sequence of the ZFN is the amino acid sequence SEQ ID NO: 79. In some embodiments, a first ZFP comprising amino acid sequences SEQ ID NOS.: 75-78 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP, and a second ZFP comprising amino acid sequences SEQ ID NOS.: 80-83 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP. In some embodiments, a first target sequence of the ZFN is the amino acid sequence SEQ ID No: 85, and a second target sequence of the ZFN is the amino acid sequence SEQ ID NO: 90. In some embodiments, a first ZFP comprising amino acid sequences SEQ ID NOS.: 86-89 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP, and a second ZFP comprising amino acid sequences SEQ ID NOS.: 91-94 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP.
In some embodiments, an intracellular domain of the modified spry1 and/or spry2 consisting essentially of the amino acid sequence SEQ ID NO: 114 or 115. In some embodiments, the modified ERBB4 has a mutant site of tyrosine phosphorylation as compared to the corresponding wild-type receptor. In some embodiments, the cell has the disruption in an endogenous gene associated with a biosynthesis or transportation pathway of foxol and a reduced amount of foxol as compared to the corresponding wild-type of the cell. In some embodiments, the disruption is made by a nuclease. In some embodiments, the disruption is made by a CRISPR associated protein 9 (Cas9). In some embodiments, the disruption is made by a Transcription activator-like effector nuclease (TALEN). In some embodiments, the disruption is made by a zinc finger nuclease (ZFN). In some embodiments, a first target sequence of the ZFN is the amino acid sequence SEQ ID No: 96 and a second target sequence of the ZFN is the amino acid sequence SEQ ID NO: 101. In some embodiments, a first ZFP comprising amino acid sequences SEQ ID NOS.: 97-100 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP, and a second ZFP comprising amino acid sequences SEQ ID NOS.: 102-105 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP.
In some embodiments, the cell overexpresses an endogenous gene associated with a biosynthesis or transportation pathway of phosphatidylinositol-specific phospholipase (PLC)-γ and an increased amount of phosphatidylinositol-specific phospholipase (PLC)-γ as compared to the corresponding wild-type of the cell. In some embodiments, the (PLC)-γ is overexpressed as compared to the corresponding wild-type of the cell. In some embodiments, a level of expression of the (PLC)-γ is greater than the average level of expression of (PLC)-γ on the cell at least about 10%, 20%, 30%, 40%, or 50%. In some embodiments, the genome of the cell comprises a polynucleotide sequence encoding the (PLC)-γ, the polynucleotide sequence operably linked to a promoter polynucleotide sequence. In some embodiments, the overexpression of (PLC)-γ is regulated by a SynNotch polypeptide such that (PLC)-γ is overexpressed in response to binding of a target antigen.
In some embodiments, the cell has the enhancement in an endogenous gene associated with a biosynthesis or transportation pathway of TLR9 and/or MyD88 and an increased amount of TLR9 and/or MyD88 as compared to the corresponding wild-type of the cell. In some embodiments, the TLR9 and/or MyD88 is overexpressed as compared to the corresponding wild-type of the cell. In some embodiments, a level of expression of the TLR9 and/or MyD88 is greater than the average level of expression of TLR9 and/or MyD88 on the cell at least about 10%, 20%, 30%, 40%, or 50%. In some embodiments, the genome of the cell comprises a polynucleotide sequence encoding the TLR9 and/or MyD88, the polynucleotide sequence operably linked to a promoter polynucleotide sequence. In some embodiments, the overexpression of TLR9 and/or MyD88 is regulated by a SynNotch polypeptide such that TLR9 and/or MyD88 is overexpressed in response to binding of a target antigen.
In some embodiments, the intracellular domain of the CAR comprises the intercellular function domain of TLR9 (TIR domain SEQ ID NO: 116. In some embodiments, TLR9 are expressed on cDCs and macrophages, which is infused into a subject who is treated with the cell. In some embodiments, the cell comprises a nucleic acid sequence encoding a constitutively active form of IRAK1/IRAK4 or IRF7 (See SEQ ID NO: 110 and 111). Association with MYD88 leads to IRAK1 phosphorylation by IRAK4 and subsequent autophosphorylation and kinase activation. Following recruitment on the activated receptor complex, phosphorylated on Thr-209, probably by IRAK4, resulting in a conformational change of the kinase domain, allowing further phosphorylations to take place. Thr-387 phosphorylation in the activation loop is required to achieve full enzymatic activity. IRAK4 is rapidly recruited by MYD88 to the receptor-signaling complex upon TLR activation to form the Myddosome together with IRAK2. Phosphorylates initially IRAK1, thus stimulating the kinase activity and intensive autophosphorylation of IRAK1. In response to a viral infection, phosphorylated on Ser-477 and Ser-479 by TBK1 and IKBKE1, phosphorylation, and subsequent activation is inhibited by vaccinia virus protein E3. In TLR7- and TLR9-mediated signaling pathway, phosphorylated by IRAK1.
Phosphatidylinositol-specific phospholipase C (PLC)-γ is a common partner of spry1 and spry2 (reference: Sprouty Proteins Inhibit Receptor-mediated Activation of Phosphatidylinositol-specific Phospholipase C), so (PLC)-γ can be used as a downstream molecule of spry protein. Cells deficient for spry1 or spry2 showed increased production of IP(3) at baseline and further increased in response to growth factor signals. Spry-PLCγ interaction was dependent on the Src homology 2 domain of PLCγ and a conserved N-terminal tyrosine residue in Spry1 and Spry2. In some embodiments, this tyrosine may be mutated to do the dominant negative of the spry protein, Y53A and Y55A, respectively.
TLR9 contributes to tumor regression by inducing cytotoxic T cell response (CTL), reducing the numbers of myeloid-derived suppressor cells (MDSCs), the tumor-associated macrophages (TAMs) and the regulatory T cells (T regs). Upon ligand binding, The TIR domain of TLR9 recruits MyD88 which forms a supramolecular complex with TNF receptor-associated factor 6 (TFAF6), Interleukin-1 receptor-associated kinases 1 and 4 (IRAK1/IRAK4), and Interferon Regulatory Factor 7 (IRF7). Once phosphorylated IRF7 translocates to the nucleus and induces the expression of type I interferon and interferon inducible genes. Stimulation of TLR9 with its ligands leads also to the activation of other transcription factors, including nuclear factor kB (NF-kB) and activator protein-1 (AP-1). (reference: the role of Toll-like receptor 9 in gynecologic cancer, 2016).
In some embodiments, CAR T cells may overexpress for TLR9 and MyD88 and/or the ordinary CAR's intracellular domain may be replaced with the TLR9′s intercellular functional domain (TIR domain), which activates the downstream signal. The downstream molecules of TLR9, IRAK1/IRAK4 and IRF7, are both Serine/threonine-protein kinase that plays a critical role in initiating innate immune response against foreign pathogens. A constitutively active form of these receptors may be used to continuously activate downstream signals. TLR9 may be expressed on conventional dendritic cells (cDCs) and macrophages, which may be infused to a subject to enhance CAR T cell therapy.
Some embodiments relate to a vector comprising one or more nucleic acid sequences listed above. In some embodiments, a lymphocyte comprises the one or more nucleic acid sequences listed above. In some embodiments, a pharmaceutical composition comprises the lymphocyte (e.g., a T cell, a NK cell, or a macrophage)
In some embodiments, the disruption in the endogenous gene or the addition of the exogenous gene are controlled by a system. For example, the disruption in the endogenous gene or the addition of the exogenous gene may be antigen-dependent. Notch receptors are transmembrane proteins that mediate cell-cell contact signaling and play a central role in development and other aspects of cell-to-cell communication. Notch receptors expressed in a receiver cell recognize their ligands (the delta family of proteins), expressed on a sending cell. The engagement of notch and delta on these contacting cells leads to two-step proteolysis of the notch receptor that ultimately causes the release of the intracellular portion of the receptor from the membrane into the cytoplasm. This released domain alters receiver cell behavior by functioning as a transcriptional regulator.
In some embodiments, a chimeric Notch receptor polypeptide may include, from N-terminal to C-terminal and in covalent linkage: an extracellular domain comprising a first member of a specific binding pair; a Notch receptor polypeptide. The Notch receptor polypeptide has a length of from 50 amino acids to 1000 amino acids, and comprises one or more ligand-inducible proteolytic cleavage sites. The chimeric Notch receptor polypeptide may further include an intracellular domain such that the first member of the specific binding pair is heterologous to the Notch receptor polypeptide, and binding of the first member of the specific binding pair to a second member of the specific binding pair induces cleavage of the Notch receptor polypeptide at the one or more ligand-inducible proteolytic cleavage sites, thereby releasing the intracellular domain. In some embodiments, the Notch receptor polypeptide has a length of from 300 amino acids to 400 amino acids. In some embodiments, the chimeric Notch receptor polypeptide comprises a linker interposed between the extracellular domain and the Notch receptor polypeptide. In some embodiments, the intracellular domain is a transcriptional activator. In some embodiments, the intracellular domain is a transcriptional repressor. In some embodiments, the intracellular domain is a site-specific nuclease. In some embodiments, the site-specific nuclease is a Cas9 polypeptide. In some embodiments, the intracellular domain is a recombinase. In some embodiments, the intracellular domain is an inhibitory immunoreceptor. In some embodiments, the intracellular domain is an activating immunoreceptor.
In some embodiments, gene overexpression or exogenous gene expression may be under control of the nuclear factor of activated T cell (NFAT)-derived minimal promoter that initiates certain transcription upon TCR- or CAR-mediated T cell activation. In the process, a protein corresponding to the certain gene may be released on CAR signaling in engineered T cells intended to accumulate to high levels in the targeted solid tumor lesion while avoiding substantial increase in a protein corresponding to the certain gene. For example, antigen engagement by the TCR or CAR—both of which utilize the CD3ζ signaling domain for downstream signaling—activated the NFAT-responsive elements, resulting in subsequent the protein transcription and triggered the protein release.
In some embodiments, the antigen binding molecule is a chimeric antigen receptor (CAR) or a T Cell Receptor (TCR). The term “Chimeric Antigen Receptor” or alternatively a “CAR” refers to a recombinant polypeptide construct comprising at least an extracellular antigen binding domain, a transmembrane domain and an intracellular signaling domain (e.g., cytoplasmic domain). In some embodiments, the domains in the CAR polypeptide construct are in the same polypeptide chain (e.g., comprising a chimeric fusion protein) or not contiguous with each other (e.g., in different polypeptide chains).
In some embodiments, the intracellular signaling domain may include a functional signaling domain derived from a stimulatory molecule and/or a co-stimulatory molecule as described above. In certain embodiments, the intracellular signaling domain includes a functional signaling domain derived from a primary signaling domain (e.g., a primary signaling domain of CD3-zeta). In other embodiments, the intracellular signaling domain further includes one or more functional signaling domains derived from at least one co-stimulatory molecule. The co-stimulatory signaling region refers to a portion of the CAR including the intracellular domain of a co-stimulatory molecule. Co-stimulatory molecules are cell surface molecules other than antigens receptors or their ligands that are required for an efficient response of lymphocytes to antigen.
Between the extracellular domain and the transmembrane domain of the CAR, there may be incorporated a spacer domain. As used herein, the term “spacer domain” generally means any oligo- or polypeptide that functions to link the transmembrane domain to, either the extracellular domain or, the cytoplasmic domain in the polypeptide chain. A spacer domain may include up to 300 amino acids, preferably 10 to 100 amino acids, and most preferably 25 to 50 amino acids.
The extracellular domain of a CAR may include an antigen binding domain (e.g., a scFv, a single domain antibody, or TCR (e.g., a TCR alpha binding domain or TCR beta binding domain)) that targets a specific tumor marker (e.g., a tumor antigen). Tumor antigens are proteins that are produced by tumor cells that elicit an immune response, particularly T-cell mediated immune responses. Tumor antigens are well known in the art and include, for example, a glioma-associated antigen, carcinoembryonic antigen (CEA), β-human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut hsp70-2, M-CSF, prostase, prostate-specific antigen (PSA), PAP, NY-ESO-1, LAGE-1a, p53, prostein, PSMA, Her2/neu, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, CD22, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor and mesothelin. For example, the tumor antigen is CD19, and the CAR thereof may be referred as CD19CAR.
In some embodiments, the extracellular ligand-binding domain comprises a scFv comprising the light chain variable (VL) region and the heavy chain variable (VH) region of a target antigen-specific monoclonal antibody joined by a flexible linker. Single chain variable region fragments are made by linking light and/or heavy chain variable regions by using a short linking peptide (Bird et al., Science 242:423-426, 1988). An example of a linking peptide is the GS linker having the amino acid sequence (GGGGS)3 (SEQ ID NO: 75), which bridges approximately 3.5 nm between the carboxy terminus of one variable region and the amino terminus of the other variable region. Linkers of other sequences have been designed and used (Bird et al., 1988, supra). In general, linkers can be short, flexible polypeptides and preferably comprised of about 20 or fewer amino acid residues. Linkers can, in turn, be modified for additional functions, such as attachment of drugs or attachment to solid supports. The single chain variants can be produced either recombinantly or synthetically. For synthetic production of scFv, an automated synthesizer can be used. For recombinant production of scFv, a suitable plasmid containing polynucleotide that encodes the scFv can be introduced into a suitable host cell, either eukaryotic, such as yeast, plant, insect or mammalian cells, or prokaryotic, such as E. coli. Polynucleotides encoding the scFv of interest can be made by routine manipulations such as ligation of polynucleotides. The resultant scFv can be isolated using standard protein purification techniques known in the art.
In embodiments, the CAR molecules described herein comprise one or more complementarity-determining regions (CDRs) for binding an antigen of interest. CDRs are part of the variable domains in immunoglobulins and T cell receptors for binding a specific antigen. There are three CDRs for each variable domain. Since there is a variable heavy domain and a variable light domain, there are six CDRs for binding an antigen. Further since an antibody has two heavy chains and two light chains, an antibody has twelve CDRs altogether for binding antigens. In embodiments, the CAR molecules described herein comprise one or more CDRs for binding a tumor.
In some embodiments, the tumor antigen includes HER2, CD19, CD20, CD22, Kappa or light chain, CD30, CD33, CD123, CD38, ROR1, ErbB3/4, EGFR, EGFRvIll, EphA2, FAP, carcinoembryonic antigen, EGP2, EGP40, mesothelin, TAG72, PSMA, NKG2D ligands, B7-H6, IL-13 receptor α 2, IL-11 receptor α, MUC1, MUC16, CA9, GD2, GD3, HMW-MAA, CD171, Lewis Y, G250/CAIX, HLA-Al MAGE A1, HLA-A2 NY-ESO-1, PSC1, folate receptor-α, CD44v7/8, 8H9, NCAM, VEGF receptors, 5T4, Fetal AchR, NKG2D ligands, CD44v6, TEM1, TEM8, or viral-associated antigens expressed by the tumor.
In some embodiments, the antigen binding molecule is a T Cell Receptor (TCR). In some embodiments, the TCR is modified TCR. In some embodiments, the TCR is derived from spontaneously occurring tumor-specific T cells in patients. In some embodiments, the TCR binds to a tumor antigen. In some embodiments, the tumor antigen comprises CEA, gp100, MART-1, p53, MAGE-A3, or NY-ESO-1. In some embodiments, the TCR comprises TCRγ and TCRδ Chains or TCRα and TCRβ chains. In some embodiments, a T cell clone that expresses a TCR with high affinity for the target antigen may be isolated. In certain embodiments, tumor-infiltrating lymphocytes (TILs) or peripheral blood mononuclear cells (PBMCs) may be cultured in the presence of antigen-presenting cells (APCs) pulsed with a peptide representing an epitope known to elicit a dominant T cell response when presented in the context of a defined HLA allele. High-affinity clones may be then selected on the basis of MHC-peptide tetramer staining and/or the ability to recognize and lyse target cells pulsed with low titrated concentrations of cognate peptide antigen. After the clone has been selected, the TCRα and TCRβ chains or TCRγ and TCRδ Chains are identified and isolated by molecular cloning. For example, for TCRα and TCRβ chains, the TCRα and TCRβ gene sequences are then used to generate an expression construct that ideally promotes stable, high-level expression of both TCR chains in human T cells. The transduction vehicle (e.g., a gammaretrovirus or lentivirus) may be then generated and tested for functionality (antigen specificity and functional avidity) and used to produce a clinical lot of the vector. An aliquot of the final product is then used to transduce the target T cell population (generally purified from patient PBMCs), which is expanded before infusion into the patient.
In some embodiments, the binding element of the CAR may include any antigen binding moiety that when bound to its cognate antigen, affects a tumor cell such that the tumor cell fails to grow, or is promoted to die or diminish.
The nucleic acid sequences coding for the desired molecules can be obtained using recombinant methods known in the art, such as, for example by screening libraries from cells expressing the gene, by deriving the gene from a vector known to include the same, or by isolating directly from cells and tissues containing the same, using standard techniques. Alternatively, the gene of interest can be produced synthetically, rather than cloned.
The embodiments of the present disclosure further relate to vectors in which a DNA of the present disclosure is inserted. Vectors derived from retroviruses such as the lentivirus are suitable tools to achieve long-term gene transfer since they allow long-term, stable integration of a transgene and its propagation in daughter cells. Lentiviral vectors have the added advantage over vectors derived from onco-retroviruses such as murine leukemia viruses in that they can transduce non-proliferating cells, such as hepatocytes. They also have the added advantage of low immunogenicity.
The expression of natural or synthetic nucleic acids encoding CARs is typically achieved by operably linking a nucleic acid encoding the CAR polypeptide or portions thereof to one or more promoters and incorporating the construct into an expression vector. The vectors can be suitable for replication and integration eukaryotes. Typical cloning vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the desired nucleic acid sequence.
Additional information related to expression synthetic nucleic acids encoding CARs and gene transfer into mammalian cells is provided in U.S. Pat. No. 8,906,682, incorporated by reference in its entirety.
Some embodiments relate to a method or use of polynucleotides encoding a CAR, a nuclease (e.g., Crispr cas9), and/or dominant negative mutant (e.g., dDn-TIGIT). The method or use includes: providing a viral particle (e.g., AAV, lentivirus or their variants) comprising a vector genome, the vector genome comprising the polynucleotide, wherein the polynucleotide is operably linked to an expression control element conferring transcription of the polynucleotide; and administering an amount of the viral particle to the subject such that the polynucleotide is expressed in the subject. In embodiments, the AAV preparation may include AAV vector particles, empty capsids and host cell impurities, thereby providing an AAV product substantially free of AAV empty capsids. More information of the administration and preparation of the viral particle may be found at the U.S. Pat. No. 9,840,719 and Milani et al., Sci. Transl. Med. 11, eaav7325 (2019) 22 May 2019, which are incorporated herein by reference.
Pharmaceutical compositions of the present disclosure may be administered in a manner appropriate to the disease to be treated (or prevented). The quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient's disease, although appropriate dosages may be determined by clinical trials.
When “an immunologically effective amount”, “an anti-tumor effective amount”, “a tumor-inhibiting effective amount”, or “therapeutic amount” is indicated, the precise amount of the compositions of the present disclosure to be administered can be determined by a physician with consideration of individual differences in age, weight, tumor size, extent of infection or metastasis, and condition of the patient (subject). It can be stated that a pharmaceutical composition comprising the T cells described herein may be administered at a dosage of 104 to 109cells/kg body weight, preferably 105to106cells/kg body weight, including all integer values within those ranges. T cell compositions may also be administered multiple times at these dosages. The cells can be administered by using infusion techniques that are commonly known in immunotherapy (see, e.g., Rosenberg et al., New Eng. J. of Med. 319:1676, 1988). The optimal dosage and treatment regime for a particular patient can readily be determined by one skilled in the art of medicine by monitoring the patient for signs of disease and adjusting the treatment accordingly. In certain embodiments, it may be desired to administer activated T cells to a subject and then subsequently redraw the blood (or have apheresis performed), collect the activated and expanded T cells, and reinfuse the patient with these activated and expanded T cells. This process can be carried out multiple times every few weeks. In certain embodiments, T cells can be activated from blood draws of from 10 cc to 400 cc. In certain embodiments, T cells are activated from blood draws of 20 cc, 30 cc, 40 cc, 50 cc, 60 cc, 70 cc, 80 cc, 90 cc, or 100 cc. Not to be bound by theory, using this multiple blood draw/multiple reinfusion protocols, may select out certain populations of T cells.
The administration of the pharmaceutical compositions described herein may be carried out in any convenient manner, including by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation. The compositions described herein may be administered to a patient subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous (i. v.) injection, or intraperitoneally. In some embodiments, the T cell compositions of the present disclosure are administered to a patient by intradermal or subcutaneous injection. In another embodiment, the T cell compositions of the present disclosure are preferably administered by i.v. injection. The compositions of T cells may be injected directly into a tumor, lymph node, or site of infection. In certain embodiments of the present disclosure, cells activated and expanded using the methods described herein, or other methods known in the art where T cells are expanded to therapeutic levels, are administered to a patient in conjunction with (e.g., before, simultaneously or following) any number of relevant treatment modalities, including but not limited to treatment with agents such as antiviral therapy, cidofovir and interleukin-2, Cytarabine (also known as ARA-C) or natalizumab treatment for MS patients or efalizumab treatment for psoriasis patients or other treatments for PML patients. In further embodiments, the T cells of the present disclosure may be used in combination with chemotherapy, radiation, immunosuppressive agents, such as cyclosporin, azathioprine, methotrexate, mycophenolate, and FK506, antibodies, or other immunoablative agents such as CAM PATH, anti-CD3 antibodies or other antibody therapies, cytoxin, fludaribine, cyclosporin, FK506, rapamycin, mycophenolic acid, steroids, FR901228, cytokines, and irradiation. These drugs inhibit either the calcium dependent phosphatase calcineurin (cyclosporine and FK506) or inhibit the p70S6 kinase that is important for growth factor induced signaling (rapamycin). (Liu et al., Cell 66:807-815, 1991; Henderson et al., Immun 73:316-321, 1991; Bierer et al., Curr. Opin. Immun 5:763-773, 1993; Isoniemi (supra)). In some embodiments, the cell compositions of the present disclosure are administered to a patient in conjunction with (e.g., before, simultaneously or following) bone marrow transplantation, T cell ablative therapy using either chemotherapy agents such as, fludarabine, external-beam radiation therapy (XRT), cyclophosphamide, or antibodies such as OKT3 or CAMPATH. In other embodiments, the cell compositions of the present disclosure are administered following B-cell ablative therapy such as agents that react with CD20, e.g., Rituxan. For example, in some embodiments, subjects may undergo standard treatment with high dose chemotherapy followed by peripheral blood stem cell transplantation. In certain embodiments, following the transplant, subjects receive an infusion of the expanded immune cells of the present disclosure. In other embodiments, expanded cells are administered before or following surgery.
The dosage of the above treatments to be administered to a patient will vary with the precise nature of the condition being treated and the recipient of the treatment. The scaling of dosages for human administration can be performed according to art-accepted practices by a physician depending on various factors.
Additional information on the methods of cancer treatment using engineered or modified T cells is provided in U.S. Pat. No. 8,906,682, incorporated by reference in its entirety.
Some embodiments relate to an in vitro method for preparing modified cells. The method may include obtaining a sample of cells from the subject. For example, the sample may include T cells or T cell progenitors. The method may further include transfecting the cells with a DNA encoding at least a CAR, culturing the population of CAR cells ex vivo in a medium that selectively enhances proliferation of CAR-expressing T cells.
In embodiments, viruses are used to deliver nucleic acids into a cell in vitro and in vivo (in a subject). Examples of viruses useful for delivery of nucleic acids into cells include retrovirus, adenovirus, herpes simplex virus, vaccinia virus, and adeno-associated virus. In embodiments, non-viral methods are used for deliverying nucleic acids into a cell. Examples of non-viral methods include electroporation, gene gun, sonoporation, magnetofection, and the use of oligonucleotides, lipoplexes, dendrimers, and inorganic nanoparticles.
In some embodiments, the sample of cells is a cryopreserved sample. In some embodiments, the sample of cells is from umbilical cord blood or a peripheral blood sample from the subject. In some embodiments, the sample of cells is obtained by apheresis or venipuncture. In some embodiments, the sample of cells is a subpopulation of T cells.
In embodiments, the sample of cells is a population of cells described herein and is used in autologous CAR T cell therapy. In embodiments, the CAR T cell therapy is allogenic CAR T cell therapy, TCR T cell therapy, and NK cell therapy.
The present disclosure is further described by reference to the following exemplary embodiments and examples. These exemplary embodiments and examples are provided for purposes of illustration only and are not intended to be limiting unless otherwise specified. Thus, the present disclosure should in no way be construed as being limited to the following exemplary embodiments and examples, but rather, should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.
EXEMPLARY EMBODIMENTSThe following are exemplary embodiments:
- 1. A modified cell comprising: an antigen binding molecule; and a disruption in an endogenous gene or an addition of exogenous gene that are associated with a biosynthesis or transportation pathway of at least one of CXCR3, SLC1A3, YAP, TIGIT, S1P1, and IL-35.
- 2. The cell of embodiment 1, wherein the antigen binding molecule comprises a chimeric antigen receptor (CAR) and/or the second antigen binding molecule is a T Cell Receptor (TCR).
- 3. The cell of embodiment 2, wherein the antigen binding molecule is the CAR comprising an extracellular domain, a transmembrane domain, and an intracellular domain, the extracellular domain binds an antigen.
- 4. The cell of embodiment 3, wherein the intracellular domain comprises a co-stimulatory signaling region that comprises an intracellular domain of a co-stimulatory molecule selected from the group consisting of CD27, CD28, 4-1BB, OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and any combination thereof.
- 5. The cell of embodiment 3, wherein the antigen is Epidermal growth factor receptor (EGFR), Variant III of the epidermal growth factor receptor (EGFRvIII), Human epidermal growth factor receptor 2 (HER2), Mesothelin (MSLN), Prostate-specific membrane antigen (PSMA), Carcinoembryonic antigen (CEA), Disialoganglioside 2 (GD2), Interleukin-13Ra2 (IL13Rα2), Glypican-3 (GPC3), Carbonic anhydrase IX (CAIX), L1 cell adhesion molecule (L1-CAM), Cancer antigen 125 (CA125), Cluster of differentiation 133 (CD133), Fibroblast activation protein (FAP), Cancer/testis antigen 1B (CTAG1B), Mucin 1 (MUC1), Folate receptor-α (FR-α) CD19, FZD10, TSHR, PRLR, Muc 17, GUCY2C, CD207, CD3, CDS, B-Cell Maturation Antigen (BCMA), or CD4.
- 6. The cell of embodiment 2, wherein the antigen binding molecule is a modified TCR.
- 7. The cell of embodiment 6, wherein the TCR is derived from spontaneously occurring tumor-specific T cells in patients.
- 8. The cell of embodiment 6, wherein the TCR binds to a tumor antigen.
- 9. The cell of embodiment 8, wherein the tumor antigen comprises CEA, gp100, MART-1, p53, MAGE-A3, or NY-ESO-1.
- 10. The cell of embodiment 8, wherein the TCR comprises TCRγ and TCRδ Chains or TCRα and TCRβ chains, or a combination thereof.
- 11. The cell of embodiment 1, wherein the cell is a T cell, a dendritic cell, a NK cell, or a macrophage cell.
- 12. The cell of any of embodiments 1-11, wherein the cell has the disruption in an endogenous gene associated with a biosynthesis or transportation pathway of CXCR2 and a reduced amount of CXCR2 as compared to the corresponding wild-type of the cell.
- 13. The cell of embodiment 12, wherein the disruption is made by a nuclease.
- 14. The cell of embodiment 12, wherein the disruption is made by a zinc finger nuclease (ZFN).
- 15. The cell of embodiment 12, wherein the disruption is made by a CRISPR associated protein 9 (Cas9).
- 16. The cell of embodiment 12, wherein the disruption is made by a Transcription activator-like effector nuclease (TALEN).
- 17. The cell of embodiment 16, wherein a target sequence of the TALEN is the amino acid sequence SEQ ID No: 29, or a left arm of the TALEN is the amino acid sequence SEQ ID No: 30, and a right arm of the TALEN is the amino acid sequence SEQ ID No: 31.
- 18. The cell of embodiment 16, wherein a target sequence of the TALEN is the amino acid sequence SEQ ID No: 32, or a left arm of the TALEN is the amino acid sequence SEQ ID No: 33, and a right arm of the TALEN is the amino acid sequence SEQ ID No: 34.
- 19. The cell of embodiment 16, wherein a target sequence of the TALEN is the amino acid sequence SEQ ID No: 35, or a left arm of the TALEN is the amino acid sequence SEQ ID No: 36, and a right arm of the TALEN is the amino acid sequence SEQ ID No: 37.
- 20. The cell of any of embodiments 1-11, wherein the cell has a nucleic acid sequence encoding modified CXCR2 that lacks a functional intracellular domain as compared to the corresponding wild-type receptor.
- 21. The cell of embodiment 20, wherein the modified CXCR2 is a dominant negative variant of CXCR2 such that the cell has an altered molecular function of CXCR2.
- 22. The cell of embodiment 20, wherein an intracellular domain of the modified CXCR2 consisting essentially of the amino acid sequence SEQ ID NO: 5 or comprising the amino acid sequence SEQ ID NO: 6.
- 23. The cell of any of embodiments 1-11, wherein the cell has the enhancement in an endogenous gene associated with a biosynthesis or transportation pathway of CXCR3 and an increased amount of CXCR2 as compared to the corresponding wild-type of the cell.
- 24. The cell of embodiment 23, wherein the CXCR3 is overexpressed as compared to the corresponding wild-type of the cell.
- 25. The cell of embodiment 24, wherein a level of expression of the CXCR3 is greater than the average level of expression of CXCR3 on the cell at least about 10%, 20%, 30%, 40%, or 50%.
- 26. The cell of embodiment 23, wherein the genome of the cell comprises a polynucleotide sequence encoding the CXCR3, the polynucleotide sequence operably linked to a promoter polynucleotide sequence.
- 27. The cell of embodiment 24, wherein the CAR an extracellular, a transmembrane domain; and an intracellular segment comprising a co-stimulatory domain and a CD3 intracellular signaling domain comprising a CXCL9/CXCL10-CXCR3 signaling motif.
- 28. The cell of any of embodiments 1-11, wherein the cell comprises a nucleic acid sequence encoding SLC1A3.
- 29. The cell of embodiment 28, wherein the cell comprises a nucleic acid sequence SEQ ID NO: Construct of SLC1A3-CART.
- 30. The cell of embodiment 28, wherein the cell has enhanced capability of uptake of glutamate.
- 31. The cell of any of embodiments 1-11, wherein the cell has a reduced amount of Yes-associated protein (YAP) as compared to a corresponding wild-type cell, wherein the modified cell has decreased Treg-mediated suppression of antitumor immunity as compared to the corresponding wild-type cell.
- 32. The cell of embodiment 31, wherein the modified T cell has a disruption in an endogenous gene associated with a biosynthesis or transportation pathway of YAP.
- 33. The cell of embodiment 32, wherein the disruption comprises a disruption of one or more exons of YAP gene.
- 34. The cell of embodiment 33, wherein the disruption of the one or more exons of YAP gene comprises a disruption of an exon of YAP gene having the nucleic acid sequence ID: 7.
- 35. The cell of embodiment 33, further comprising a TALEN targeting the nucleic acid sequence ID: 38.
- 36. The cell of embodiment 35, wherein the TALEN comprise a left arm comprising the nucleic acid sequence ID: 39 and a right arm comprising the nucleic acid SEQ ID NO: 40.
- 37. The cell of any of embodiments 1-11, wherein the cell has a nucleic acid sequence that encodes a modified receptor that directly or indirectly activate YAP activity, the modified receptor lacking a functional intracellular domain, and the modified receptor and the antigen binding molecule are expressed as gene products that are separate polypeptides.
- 38. The cell of embodiment 37, wherein the modified receptor is ERBB4, CD44, or a G12/13-coupled receptor that lacks a functional intracellular domain as compared to the corresponding wild-type receptor.
- 39. The cell of embodiment 38, wherein the G12/13-coupled receptor comprises one of adrenergic receptor al B, LPA receptors, purinergic receptors, 5-hydroxytryptamine receptor 4, muscarinic acetylcholine receptor M1, adenosine receptor A1A, angiontensin II receptor, free fatty acid receptor 1, platelet-activating factor receptor, thromboxane A2, frizzled homolog D4, complement component 3a receptor 1, estrogen receptor 1, glutamate receptor metabotropic 2, opioid receptor D1, secretin receptor, thyroid-stimulating hormone receptor, gastrin-releasing peptide receptor, melanocortin receptor 1, somatostatin receptor 1, prostaglandin E receptor 2, and bombesin-like receptor 3.
- 40. The cell of embodiment 37, wherein the modified receptor is a modified ERBB4.
- 41. The cell of embodiment 40, wherein the modified ERBB4 consist essentially of the nucleic acid sequence ID: 11.
- 42. The of embodiment 37, wherein the modified receptor is a modified LPAR1.
- 43. The cell of embodiment 42, wherein the modified LPAR1 consist essentially the nucleic acid sequence ID: 14.
- 44. The of embodiment 37, wherein the modified receptor is a modified CD44.
- 45. The cell of embodiment 44, wherein the modified CD44 consist essentially the nucleic acid sequence ID: 17.
- 46. The cell of embodiment 44, wherein the modified ERBB4 has a mutant site of tyrosine phosphorylation as compared to the corresponding wild-type receptor.
- 47. The T lymphocyte cell of embodiment 46, wherein the modified receptor is a dominant negative of ERBB4 receptor.
- 48. The lymphocyte T cell of embodiment 37, wherein the modified receptor is a dominant negative variant of a receptor of the ERBB4, CD44, or G12/13-coupled receptor.
- 49. The cell of any of embodiments 1-11, wherein the cell has a nucleic acid sequence encoding modified TIGIT that lacks a functional intracellular domain as compared to the corresponding wild-type receptor.
- 50. The cell of embodiment 49, wherein the modified TIGIT is a dominant negative variant of TIGIT such that the cell has an altered molecular function of TIGIT.
- 51. The cell of embodiment 49, wherein an intracellular domain of the modified TIGIT consisting essentially of the amino acid sequence SEQ ID NO: 19 or comprising the amino acid sequence SEQ ID: 20.
- 52. The cell of any of embodiments 1-11, wherein the cell comprises a nucleic acid sequence encoding S1P1.
- 53. The cell of embodiment 52, wherein the cell comprises a nucleic acid sequence SEQ ID NO: Construct of S1P1-CART.
- 49. The cell of any of embodiments 1-11, wherein the cell has a nucleic acid sequence encoding a modified IL-35 receptor that lacks a functional intracellular domain as compared to the corresponding wild-type receptor.
- 50. The cell of embodiment 49, wherein the modified IL-35 receptor is a dominant negative variant of IL-35 receptor such that the cell has an altered molecular function of IL-35 receptor.
- 51. The cell of embodiment 50, wherein the modified receptor is gp130 or IL-12Rβ2 receptor that lacks a functional intracellular domain as compared to the corresponding wild-type receptor
- 51. The cell of embodiment 49, wherein an intracellular domain of the modified IL-35 receptor consisting essentially of the amino acid sequence SEQ ID NO: 24 or 27 or comprising the amino acid sequence SEQ ID NO: 25 or 28.
- 52. A pharmaceutical composition comprising the population of the CAR cells of any of embodiments 1-51.
- 53. A method of causing or eliciting T cell response in a subject in need thereof and/or treating a tumor of the subject, the method comprising administering an effective amount of the composition of embodiment 52 to the subject.
- 54. The modified cell, the method, the pharmaceutical composition, the cell of one of embodiments 1-53, wherein the disruption in an endogenous gene or the addition of exogenous gene is associated with an oxygen-sensitive polypeptide domain.
- 55. The modified cell, the method, the pharmaceutical composition, the cell of embodiment
- 54, wherein the oxygen-sensitive polypeptide domain comprises HIF VHL binding domain.
- 56. The modified cell, the method, the pharmaceutical composition, the cell of one of embodiments 1-53, wherein the disruption in an endogenous gene or the addition of exogenous gene is regulated by a promoter comprising a binding site for a transcription modulator that modulates the expression and/or secretion of the therapeutic agent in the cell.
- 57. The modified cell, the method, the pharmaceutical composition, the cell of embodiment 56, wherein the transcription modulator is or includes Hif1a, NFAT, FOXP3, and/or NFkB.
- 58. The cell of any of embodiments 1-11, wherein the cell has the disruption in an endogenous gene associated with a biosynthesis or transportation pathway of spry1 and/or spry2 and a reduced amount of spry1 and/or spry2as compared to the corresponding wild-type of the cell.
- 59. The cell of embodiment 58, wherein the disruption is made by a nuclease.
- 60. The cell of embodiment 58, wherein the disruption is made by a CRISPR associated protein 9 (Cas9).
- 61. The cell of embodiment 58, wherein the disruption is made by a Transcription activator-like effector nuclease (TALEN).
- 62. The cell of embodiment 58, wherein the disruption is made by a zinc finger nuclease (ZFN).
- 63. The cell of embodiment 62, wherein a first target sequence of the ZFN is the amino acid sequence SEQ ID No: 74, and a second target sequence of the ZFN is the amino acid sequence SEQ ID NO: 79.
- 64. The cell of embodiment 62, wherein a first ZFP comprising amino acid sequences SEQ ID NOS.: 75-78 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP, and a second ZFP comprising amino acid sequences SEQ ID NOS.: 80-83 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP.
- 65. The cell of embodiment 62, wherein a first target sequence of the ZFN is the amino acid sequence SEQ ID No: 85, and a second target sequence of the ZFN is the amino acid sequence SEQ ID NO: 90.
- 66. The cell of embodiment 64, wherein a first ZFP comprising amino acid sequences SEQ ID NOS.: 86-89 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP, and a second ZFP comprising amino acid sequences SEQ ID NOS.: 91-94 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP.
- 67. The cell of embodiment 58, wherein the modified spry1 is a dominant negative variant of spry1 such that the cell has an altered molecular function of spry1.
- 68. The cell of embodiment 58, wherein the modified spry2 is a dominant negative variant of spry2 such that the cell has an altered molecular function of spry2.
- 69. The cell of embodiment 67, wherein an intracellular domain of the modified spry1 and/or spry2 consisting essentially of the amino acid sequence SEQ ID NO: 114 or 115.
- 70. The cell of embodiment 67, wherein the modified ERBB4 has a mutant site of tyrosine phosphorylation as compared to the corresponding wild-type receptor.
- 71. The cell of embodiment 60, wherein the cell has the disruption in an endogenous gene associated with a biosynthesis or transportation pathway of foxol and a reduced amount of foxol as compared to the corresponding wild-type of the cell.
- 72. The cell of embodiment 71, wherein the disruption is made by a nuclease.
- 73. The cell of embodiment 71, wherein the disruption is made by a CRISPR associated protein 9 (Cas9).
- 74. The cell of embodiment 71, wherein the disruption is made by a Transcription activator-like effector nuclease (TALEN).
- 75. The cell of embodiment 71, wherein the disruption is made by a zinc finger nuclease (ZFN).
- 76. The cell of embodiment 75, wherein a first target sequence of the ZFN is the amino acid sequence SEQ ID No: 96 and a second target sequence of the ZFN is the amino acid sequence SEQ ID NO: 101.
- 77. The cell of embodiment 75, wherein a first ZFP comprising amino acid sequences SEQ ID NOS.: 97-100 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP, and a second ZFP comprising amino acid sequences SEQ ID NOS.: 102-105 ordered from a N-terminal of the first ZFP to a C-terminal of the first ZFP.
- 78. The cell of any of embodiments 1-11, wherein the cell has the enhancement in an endogenous gene associated with a biosynthesis or transportation pathway of phosphatidylinositol-specific phospholipase (PLC)-γ and an increased amount of phosphatidylinositol-specific phospholipase (PLC)-γ as compared to the corresponding wild-type of the cell.
- 79. The cell of embodiment 78, wherein the (PLC)-γ is overexpressed as compared to the corresponding wild-type of the cell.
- 80. The cell of embodiment 78, wherein a level of expression of the (PLC)-γ is greater than the average level of expression of (PLC)-γ on the cell at least about 10%, 20%, 30%, 40%, or 50%.
- 81. The cell of embodiment 78, wherein the genome of the cell comprises a polynucleotide sequence encoding the (PLC)-γ, the polynucleotide sequence operably linked to a promoter polynucleotide sequence.
- 82. The cell of embodiment 78, wherein the overexpression of (PLC)-γ is regulated by a SynNotch polypeptide such that (PLC)-γ is overexpressed in response to binding of a target antigen.
- 83. The cell of any of embodiments 1-11, wherein the cell has the enhancement in an endogenous gene associated with a biosynthesis or transportation pathway of TLR9 and/or MyD88 and an increased amount of TLR9 and/or MyD88 as compared to the corresponding wild-type of the cell.
- 84. The cell of embodiment 83, wherein the TLR9 and/or MyD88 is overexpressed as compared to the corresponding wild-type of the cell.
- 85. The cell of embodiment 83, wherein a level of expression of the TLR9 and/or MyD88 is greater than the average level of expression of TLR9 and/or MyD88 on the cell at least about 10%, 20%, 30%, 40%, or 50%.
- 86. The cell of embodiment 83, wherein the genome of the cell comprises a polynucleotide sequence encoding the TLR9 and/or MyD88, the polynucleotide sequence operably linked to a promoter polynucleotide sequence.
- 87. The cell of embodiment 83, wherein the overexpression of TLR9 and/or MyD88 is regulated by a SynNotch polypeptide such that TLR9 and/or MyD88 is overexpressed in response to binding of a target antigen.
- 88. The cell of any of embodiments 1-11, wherein the intracellular domain of the CAR comprises the intercellular function domain of TLR9 (TIR domain SEQ ID NO: 116.
- 89. The cell of any of embodiments 1-11, wherein TLR9 are expressed on cDCs and macrophages, which is infused into a subject who is treated with the cell.
- 90. The cell of embodiment 83, wherein the cell comprises a nucleic acid sequence encoding a constitutively active form of IRAK1/IRAK4 or IRF7 (See SEQ ID NO: 110 and 111).
- 91. A modified cell engineered to express an antigen binding molecule, wherein expression and/or function of one or more genes in the modified cell has been 1) enhanced, or 2) reduced or eliminated.
- 92. The modified cell of embodiment 91, wherein the one or more genes comprise at least one of CXCR3, SLC1A3, YAP, TIGIT, S1P1, and IL-35.
- 93. The modified cell of embodiment 91, wherein the one or more genes are CXCR3 and/or TIGIT.
- 94. A modified cell engineered to express an antigen binding molecule, wherein expression and/or function of TIGIT in the modified cell has been reduced or eliminated.
- 95. A modified cell engineered to express an antigen binding molecule, wherein expression and/or function of CXCR3 in the modified cell has been enhanced.
- 96. The modified cell of one of embodiments 91-94, wherein the antigen binding molecule is chimeric antigen receptor (CAR), which comprises an antigen-binding domain, a transmembrane domain, and an intracellular signaling domain.
- 97. The modified cell of embodiment 96, wherein the antigen-binding domain binds to a tumor antigen is selected from a group consisting of: TSHR, CD19, CD123, CD22, CD30, CD171, CS-1, CLL-1, CD33, EGFRvIII, GD2, GD3, BCMA, Tn Ag, PSMA, ROR1, FLT3, FAP, TAG72, CD38, CD44v6, CEA, EPCAM, B7H3, KIT, IL-13Ra2, Mesothelin, IL-11Ra, PSCA, PRSS21, VEGFR2, LewisY, CD24, PDGFR-beta, SSEA-4, CD20, Folate receptor alpha, ERBB2 (Her2/neu), MUC1, EGFR, NCAM, Prostase, PAP, ELF2M, Ephrin B2, IGF-I receptor, CAIX, LMP2, gp100, bcr-abl, tyrosinase, EphA2, Fucosyl GM1, sLe, GM3, TGS5, HMWMAA, o-acetyl-GD2, Folate receptor beta, TEM1/CD248, TEM7R, CLDN6, GPRC5D, CXORF61, CD97, CD179a, ALK, Polysialic acid, PLAC1, GloboH, NY-BR-1, UPK2, HAVCR1, ADRB3, PANX3, GPR20, LY6K, OR51E2, TARP, WT1, NY-ESO-1, LAGE-1a, MAGE-A1, legumain, HPV E6, E7, MAGE A1, ETV6-AML, sperm protein 17, XAGE1, Tie 2, MAD-CT-1, MAD-CT-2, Fos-related antigen 1, p53, p53 mutant, prostein, survivin and telomerase, PCTA-1/Galectin 8, MelanA/MART1, Ras mutant, hTERT, sarcoma translocation breakpoints, ML-IAP, ERG (TMPRSS2 ETS fusion gene), NA17, PAX3, Androgen receptor, Cyclin B1, MYCN, RhoC, TRP-2, CYP1B1, BORIS, SART3, PAX5, OY-TES1, LCK, AKAP-4, SSX2, RAGE-1, human telomerase reverse transcriptase, RU1, RU2, intestinal carboxyl esterase, mut hsp70-2, CD79a, CD79b, CD72, LAIR1, FCAR, LILRA2, CD300LF, CLEC12A, BST2, EMR2, LY75, GPC3, FCRL5, and IGLL1.
- 98. The modified cell of one of embodiments 96 and 97, wherein the intracellular signaling domain comprises a co-stimulatory signaling domain, or a primary signaling domain and a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), CD160, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, NKp44, NKp30, NKp46, and NKG2D.
- 99. The modified cell of one of embodiments 91-94, wherein the antigen binding molecule is a modified TCR.
- 100. The modified cell of embodiment 99, wherein the TCR is derived from spontaneously occurring tumor-specific T cells in patients.
- 101. The modified cell of embodiment 109 wherein the TCR binds to a tumor antigen.
- 102. The modified cell of embodiment 101, wherein the tumor antigen comprises CEA, gp100, MART-1, p53, MAGE-A3, or NY-ESO-1.
- 103. The modified cell of embodiment 102, wherein the TCR comprises TCRγ and TCRδ Chains or TCRα and TCRβ chains, or a combination thereof.
- 104. The modified cell of any of the preceding embodiments, wherein the cell is an immune effector cell (e.g., a population of immune effector cells).
- 105. The modified cell of embodiment 104, wherein the immune effector cell is a T cell or an NK cell.
- 106. The modified cell of embodiment 105, wherein the immune effector cell is a T cell.
- 107. modified cell of embodiment 106, wherein the T cell is a CD4+ T cell, a CD8+ T cell, or a combination thereof.
- 108. The modified cell of any of the preceding embodiments, wherein the cell is a human cell.
- 109. The modified cell of any of the preceding embodiments, wherein the modified cell comprises an inhibitor of expression or function of the one or more genes.
- 110. The modified cell of embodiment 109, wherein the inhibitor is (1) a gene editing system targeted to one or more sites within the gene encoding the one or more genes or a corresponding regulatory elements; (2) nucleic acid encoding one or more components of a gene editing system of the one or more genes; or (3) combinations thereof.
- 111. A pharmaceutical composition comprising the population of the cells of any of embodiments 91-110.
- 112. A method of causing or eliciting T cell response in a subject in need thereof and/or treating a tumor of the subject, the method comprising administering an effective amount of the composition of embodiment 113 to the subject.
- 113. The modified cell, the method, the pharmaceutical composition, the cell of one of embodiments 58-21, wherein the enhanced expression and/or function of the one or more genes is implemented by introducing a nucleic acid sequence of the one or more genes, which is present in the modified cell in a recombinant DNA construct, in an mRNA, or in a viral vector.
- 114. The modified cell, the method, the pharmaceutical composition, the cell of one of embodiments 91-112, wherein the reduced of expression and/or function of the one or more genes is implemented by introducing a nucleic acid sequence encoding a dominant negative form of the one or more genes, and nucleic acid sequence is present in the modified cell in a recombinant DNA construct, in an mRNA, or in a viral vector.
- 115. The modified cell, the method, the pharmaceutical composition, the cell of one of embodiments 113 and 114, wherein the nucleic acid sequence is an mRNA, which is not integrated into the genome of the modified cell.
- 116. The modified cell, the method, the pharmaceutical composition, the cell of one of embodiments 113-115, wherein the nucleic acid sequence is associated with an oxygen-sensitive polypeptide domain.
- 117. The modified cell, the method, the pharmaceutical composition, the cell of embodiment 116, wherein the oxygen-sensitive polypeptide domain comprises HIF VHL binding domain.
- 118. The modified cell, the method, the pharmaceutical composition, the cell of one of embodiments 113-115, wherein the nucleic acid sequence is regulated by a promoter comprising a binding site for a transcription modulator that modulates the expression and/or secretion of the therapeutic agent in the cell.
- 119. The modified cell, the method, the pharmaceutical composition, the cell of embodiment 118, wherein the transcription modulator is or includes Hif1a, NFAT, FOXP3, and/or NFkB.
Corresponding sequences described in EXAMPLES are listed in Table 1 below. 293T cells were infected by lentiviruses containing CXCL9/CXCL10 to express CXCL9 and CXCL10. Anti-CXCL9/CXCL10 antibodies were used to detect the expression. These cells were then added as substrate cells for migration assay. Lentiviruses of CXCL9 and CXCL10 were separately packaged with a lentiviral plasmid containing CXCL9 or CXCL10. Fresh 1×106 293T-wt cells were infected with CXCL9 or CXCL10 at a ratio of a multiplicity of infection (MOI) 1-50. After neutralizing with 10% DMEM, 5×105 cells were stained with 1 ug of CXCL9/CXCL10 antibodies. Results are shown in
Ligands of CXCR3 include CXCL9 and CXCL10. hCD19CAR and hCD19CAR-CXCR3 cells were prepared from healthy volunteers' fresh cells and cultured to expand to day7. 5×105 293T-wt, 293T with CXCL9, 293T with CXCL10 cells (thereafter Testing Cells) were plated to the bottom of the Transwell plate at day 6. At day7, 2×106 hCD19CAR and hCD19CAR-CXCR3 cells were added to the upper part of transwell containing and not containing Testing Cells. The number of cells migrating to the bottom of each group was counted 24 hours after the CART cells were added. Results are shown in
After antigen stimulation, CD19CART cells activate T cells. Activated T cells up-regulate CD137 in a short period and release cytokines such as IFNγ/NFα to cause apoptosis and to kill tumor cells. T cells (NT), hCD19CAR, and hCD19CAR-CXCR3 cells were prepared from healthy volunteers' fresh cells. When cultured and expanded to day7, fresh 2×106 NT cells, hCD19CAR, and hCD19CAR-CXCR3 were co-cultured with 2×106 CD19+NALM6 cells. After 24 hours, the cells and supernatant were taken to detect: cell numbers of CD19+ cells, CD137 expression of T cells, expression of CAR, and amounts of IFNγ and TNFα factors released in the supernatant. Results are shown in
Lentiviral plasmids containing CD155-p2A-GFP were constructed and packaged into lentiviruses using the third-generation lentiviral packaging system and the transfection reagent PElpro. Fresh 1×106 nalm6-wt cells were infected with CD155-p2A-GFP lentiviruses at a ratio of MOI 1-50. CD155 antibody was used to detect expression of CD155-p2A-GFPusing flow cytometer. Results are shown in
NT, hCD19CAR, hCD19 CAR-wtTIGIT, and hCD19 CAR-Dn-TIGITCAR cells were prepared from healthy volunteers' fresh cells and cultured and expanded to day7. On day7, fresh 2×106 NT, hCD19CAR and hCD19 CAR-wtTIGIT, hCD19 CAR-CAR-Dn-TIGIT cells were co-cultured with NALM6-CD155 cells with a tumor-CART ratio of 3-1 and 1-1. 1×106 hCD19CAR, hCD19 CAR-wtTIGIT, and hCD19 CAR-Dn-TIGIT cells were taken to measure the expression of hCAR and TIGIT using flow cytometry. 24 hours after the coluturing, cells and supernatant to measure killing of tumor cells (CD19 Positive cells), and the IFNγ and TNFα factors release were measured. As shown in
Claims
1. A modified cell engineered to express an antigen binding molecule, wherein expression and/or function of CXCR3 in the modified cell has been enhanced, and/or expression and/or function of TIGIT in the modified cell has been reduced or eliminated.
2. The modified cell of claim 1, wherein the antigen binding molecule is a chimeric antigen receptor (CAR), which comprises an antigen binding domain, a transmembrane domain, and an intracellular signaling domain.
3. The modified cell of claim 2, wherein the antigen binding domain binds to a tumor antigen selected from a group consisting of: TSHR, CD19, CD123, CD22, CD30, CD171, CS-1, CLL-1, CD33, EGFRvIII, GD2, GD3, BCMA, Tn Ag, PSMA, ROR1, FLT3, FAP, TAG72, CD38, CD44v6, CEA, EPCAM, B7H3, KIT, IL-13Ra2, Mesothelin, IL-11Ra, PSCA, PRSS21, VEGFR2, LewisY, CD24, PDGFR-beta, SSEA-4, CD20, Folate receptor alpha, ERBB2 (Her2/neu), MUC1, EGFR, NCAM, Prostase, PAP, ELF2M, Ephrin B2, IGF-I receptor, CAIX, LMP2, gp100, bcr-abl, tyrosinase, EphA2, Fucosyl GM1, sLe, GM3, TGS5, HMWMAA, o-acetyl-GD2, Folate receptor beta, TEM1/CD248, TEM7R, CLDN6, GPRC5D, CXORF61, CD97, CD179a, ALK, Polysialic acid, PLAC1, GloboH, NY-BR-1, UPK2, HAVCR1, ADRB3, PANX3, GPR20, LY6K, OR51E2, TARP, WT1, NY-ESO-1, LAGE-1a, MAGE-A1, legumain, HPV E6, E7, MAGE A1, ETV6-AML, sperm protein 17, XAGE1, Tie 2, MAD-CT-1, MAD-CT-2, Fos-related antigen 1, p53, p53 mutant, prostein, survivin and telomerase, PCTA-1/Galectin 8, MelanA/MART1, Ras mutant, hTERT, sarcoma translocation breakpoints, ML-IAP, ERG (TMPRSS2 ETS fusion gene), NA17, PAX3, Androgen receptor, Cyclin B1, MYCN, RhoC, TRP-2, CYP1B1, BORIS, SART3, PAX5, OY-TES1, LCK, AKAP-4, SSX2, RAGE-1, human telomerase reverse transcriptase, RU1, RU2, intestinal carboxyl esterase, mut hsp70-2, CD79a, CD79b, CD72, LAIR1, FCAR, LILRA2, CD300LF, CLEC12A, BST2, EMR2, LY75, GPC3, FCRL5, and IGLL1.
4. The modified cell of claim 2, wherein the intracellular signaling domain comprises a co-stimulatory signaling domain or a primary signaling domain, and a co-stimulatory signaling domain, wherein the co-stimulatory signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), CD160, CD19, CD4, CD8alpha, CD8beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Ly108), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, NKp44, NKp30, NKp46, and NKG2D.
5. The modified cell of claim 1, wherein the antigen binding molecule is a modified TCR.
6. The modified cell of claim 5, wherein the TCR is derived from spontaneously occurring tumor-specific T cells in subjects.
7. The modified cell of claim 1, wherein the modified cell is a T cell.
8. The modified cell of claim 1, wherein the modified cell comprises a dominant negative variant of TIGIT, wherein the cell has an altered molecular function of TIGIT.
9. The modified cell of claim 8, wherein an intracellular domain of the modified TIGIT consisting essentially of the amino acid sequence SEQ ID NO: 19 or comprising the amino acid sequence SEQ ID: 20.
10. The modified cell of claim 8, wherein the modified cell comprises a nucleic acid sequence encoding the modified TIGIT, and the nucleic acid is associated with an oxygen-sensitive polypeptide domain.
11. The modified cell of claim 10 wherein the oxygen-sensitive polypeptide domain comprises HIF VHL binding domain.
12. The modified cell of claim 10, wherein the nucleic acid sequence is regulated by a promoter comprising a binding site for a transcription modulator that modulates the expression and/or secretion of the therapeutic agent in the cell.
13. The modified cell of claim 12, wherein the transcription modulator is or includes Hif1a, NFAT, FOXP3, and/or NFkB.
14. The modified cell of claim 1, wherein the modified cell comprises a nucleic acid sequence encoding CXCR3.
15. The modified cell of claim 14, wherein the nucleic acid sequence is or comprises SEQ ID NO: 125.
16. The modified cell of claim 14, wherein the modified cell comprises a nucleic acid sequence encoding the modified TIGIT, and the nucleic acid is associated with an oxygen-sensitive polypeptide domain.
17. The modified cell of claim 15 wherein the oxygen-sensitive polypeptide domain comprises HIF VHL binding domain.
18. The modified cell of claim 14, wherein the nucleic acid sequence is regulated by a promoter comprising a binding site for a transcription modulator that modulates the expression and/or secretion of the therapeutic agent in the cell.
19. The modified cell of claim 18, wherein the transcription modulator is or includes Hif1a, NFAT, FOXP3, and/or NFkB.
20. A method of eliciting a T cell response in a subject in need thereof and/or treating a tumor of in a subject, the method comprising administering an effective amount of the composition comprising the population of the modified cells of claim 1 to the subject.
Type: Application
Filed: Aug 29, 2019
Publication Date: Mar 5, 2020
Patent Grant number: 11701385
Applicant: Innovative Cellular Therapeutics Co., Ltd. (Shanghai)
Inventors: Zhiyuan Cao (Shanghai), Chengfei Pu (Shanghai), Lei Xiao (Shanghai), Zhao Wu (Shanghai)
Application Number: 16/555,198
